Structure of the dodecahedral penton particle from human adenovirus type 3.

The sub-viral dodecahedral particle of human adenovirus type 3, composed of the viral penton base and fiber proteins, shares an important characteristic of the entire virus: it can attach to cells and penetrate them. Structure determination of the fiberless dodecahedron by cryo-electron microscopy to 9 Angstroms resolution reveals tightly bound pentamer subunits, with only minimal interfaces between penton bases stabilizing the fragile dodecahedron. The internal cavity of the dodecahedron is approximately 80 Angstroms in diameter, and the interior surface is accessible to solvent through perforations of approximately 20 Angstroms diameter between the pentamer towers. We observe weak density beneath pentamers that we attribute to a penton base peptide including residues 38-48. The intact amino-terminal domain appears to interfere with pentamer-pentamer interactions and its absence by mutation or proteolysis is essential for dodecamer assembly. Differences between the 9 Angstroms dodecahedron structure and the adenovirus serotype 2 (Ad2) crystallographic model correlate closely with differences in sequence. The 3D structure of the dodecahedron including fibers at 16 Angstroms resolution reveals extra density on the top of the penton base that can be attributed to the fiber N terminus. The fiber itself exhibits striations that correlate with features of the atomic structure of the partial Ad2 fiber and that represent a repeat motif present in the amino acid sequence. These new observations offer important insights into particle assembly and stability, as well as the practicality of using the dodecahedron in targeted drug delivery. The structural work provides a sound basis for manipulating the properties of this particle and thereby enhancing its value for such therapeutic use.

The cellular receptor to human rhinovirus 2 binds around the 5-fold axis and not in the canyon: a structural view.

Human rhinovirus serotype 2 (HRV2) belongs to the minor group of HRVs that bind to members of the LDL-receptor family including the very low density lipoprotein (VLDL)-receptor (VLDL-R). We have determined the structures of the complex between HRV2 and soluble fragments of the VLDL-R to 15 A resolution by cryo-electron microscopy. The receptor fragments, which include the first three ligand-binding repeats of the VLDL-R (V1-3), bind to the small star-shaped dome on the icosahedral 5-fold axis. This is in sharp contrast to the major group of HRVs where the receptor site for ICAM-1 is located at the base of a depression around each 5-fold axis. Homology models of the three domains of V1-3 were used to explore the virus-receptor interaction. The footprint of VLDL-R on the viral surface covers the BC- and HI-loops on VP1.

Flexibility of the major antigenic loop of foot-and-mouth disease virus bound to a Fab fragment of a neutralising antibody: structure and neutralisation.

The interaction of foot-and-mouth disease virus (FMDV) serotype C (clone C-S8c1) with a strongly neutralising monoclonal antibody (MAb) 4C4 has been studied by combining data from cryoelectron microscopy and x-ray crystallography. The MAb 4C4 binds to the exposed flexible GH-loop of viral protein 1 (VP1), which appears to retain its flexibility, allowing movement of the bound Fab. This is in striking contrast to MAb SD6, which binds to the same GH-loop of VP1 but exhibits no movement of the bound Fab when observed under identical conditions. However, MAbs 4C4 and SD6 have very similar neutralisation characteristics. The known atomic structure of FMDV C-S8c1 and that of the 4C4 Fab cocrystallised with a synthetic peptide corresponding to the GH-loop of VP1 were fitted to the cryoelectron microscope density map. The best fit of the 4C4 Fab is compatible only with monovalent binding of the MAb in agreement with the neutralisation data on 4C4 MAbs, Fab2s, and Fabs. The position of the bound GH-loop is related to other known positions of this loop by a hinge rotation about the base of the loop. The 4C4 Fab appears to interact almost exclusively with the G-H loop of VP1, making no other contacts with the viral capsid.

Structure of a neutralizing antibody bound monovalently to human rhinovirus 2.

The structure of a complex between human rhinovirus 2 (HRV2) and the Fab fragment of neutralizing monoclonal antibody (MAb) 3B10 has been determined to 25-A resolution by cryoelectron microscopy and three-dimensional reconstruction techniques. The footprint of 3B10 on HRV2 is very similar to that of neutralizing MAb 8F5, which binds bivalently across the icosahedral twofold axis. However, the 3B10 Fab fragment (Fab-3B10) is bound in an orientation, inclined at approximately 45 degrees to the surface of the virus capsid, which is compatible only with monovalent binding of the antibody. The canyon around the fivefold axis is not directly obstructed by the bound Fab. The X-ray structures of a closely related HRV (HRV1A) and a Fab fragment were fitted to the density maps of the HRV2-Fab-3B10 complex obtained by cryoelectron microscope techniques. The footprint of 3B10 on the viral surface is largely on VP2 but also covers the VP3 loop centered on residue 3064 and the VP1 loop centered on residue 1267. MAb 3B10 can interact directly with VP2 residue 2164, the site of an escape mutation on VP2, and with VP1 residues 1264 to 1267, the site of a deletion escape mutation. Deletion of these residues shortens the VP1 loop, moving it away from the MAb binding site. All structural and biochemical evidence indicates that MAb 3B10 binds to a conformation epitope on HRV2.

Structure of Broadhaven virus by cryoelectron microscopy: correlation of structural and antigenic properties of Broadhaven virus and bluetongue virus outer capsid proteins.

The three-dimensional structure of Broadhaven virus (BRDV) has been determined to 23 A resolution by cryoelectron microscopy and image processing. As predicted from sequence homology, the BRDV structure resembles that of bluetongue virus (BTV) with the notable exception of one of the outer shell proteins. The cores of BRDV and BTV are identical at medium resolution; they have a diameter of 710 A and the VP7 trimers are arranged on a T = 13 icosahedral lattice. The outer shell proteins, VP5 of BRDV and BTV, have roughly the same molecular weight while VP4 of BRDV is only half the molecular weight of the corresponding VP2 of BTV. This size difference allows unambiguous determination of the identity of the triskelion shape as trimers of VP4 of BRDV (VP2 of BTV). The VP4 of BRDV sits on the VP7 trimers and projects outwards 40 A, giving the capsid an overall diameter of 790 A. This contrasts with VP2 of BTV, which projects outwards 95 A to give the capsid a diameter of 900 A. The difference in accessibility of the outer shell proteins of BRDV and BTV correlates with the difference in antigenic properties of these viral proteins. The shape of the BRDV VP5 indicates that it too is a trimer, thus implying that there are 360 copies of VP5 and 180 copies of VP4 per virion.

Bivalent binding of a neutralising antibody to a calicivirus involves the torsional flexibility of the antibody hinge.

The structure of a complex between rabbit haemorrhagic disease virus (RHDV) virus-like particles (VLPs) and a neutralising monoclonal antibody mAb-E3 has been determined at low resolution by cryo-electron microscopy and three-dimensional (3-D) reconstruction techniques. The atomic co-ordinates of an Fab were fitted to the cryo-electron microscope density map to produce a binding model. The VLP has a T = 3 icosahedral lattice consisting of a hollow spherical shell with 90 protruding arches. Each dimeric arch presents two mAb binding sites; however, steric hindrance between the variable domains of the Fabs prevents the occupation of both sites simultaneously. Thus the maximum mAb occupation is 50%. Once a mAb is bound to one site it may bind to either of two neighbouring sites related by a local 3-fold axis. The mAbs are bound bivalently on epitopes not related by a 2-fold symmetry axis. This binding geometry implies a torsional flexibility of the mAb hinge region, involving a 60 degrees rotation of one Fab arm with respect to the other. Owing to extreme flexibility of the hinge region, the Fc domains occupy random orientations and are not visible in the reconstruction. The bivalent attachment of mAb-E3 to RHDV suggests that the neutralisation mechanism(s) involves inhibition of viral decapsidation and/or the inhibition of binding to the receptor.

Structure of the complex of an Fab fragment of a neutralizing antibody with foot-and-mouth disease virus: positioning of a highly mobile antigenic loop.

Data from cryo-electron microscopy and X-ray crystallography have been combined to study the interactions of foot-and-mouth disease virus serotype C (FMDV-C) with a strongly neutralizing monoclonal antibody (mAb) SD6. The mAb SD6 binds to the long flexible GH-loop of viral protein 1 (VP1) which also binds to an integrin receptor. The structure of the virus-Fab complex was determined to 30 A resolution using cryo-electron microscopy and image analysis. The known structure of FMDV-C, and of the SD6 Fab co-crystallized with a synthetic peptide corresponding to the GH-loop of VP1, were fitted to the cryo-electron microscope density map. The SD6 Fab is seen to project almost radially from the viral surface in an orientation which is only compatible with monovalent binding of the mAb. Even taking into account the mAb hinge and elbow flexibility, it is not possible to model bivalent binding without severely distorting the Fabs. The bound GH-loop is essentially in what has previously been termed the 'up' position in the best fit Fab orientation. The SD6 Fab interacts almost exclusively with the GH-loop of VP1, making very few other contacts with the viral capsid. The position and orientation of the SD6 Fab bound to FMDV-C is in accord with previous immunogenic data.

Structural study of the response regulator HupR from Rhodobacter capsulatus. Electron microscopy of two-dimensional crystals on a nickel-chelating lipid.

Two-dimensional crystals of the histidine-tagged-HupR protein, a transcriptional regulator from the photosynthetic bacterium Rhodobacter capsulatus, were obtained upon specific interaction with a Ni2+-chelated lipid monolayer. HupR is a response regulator of the NtrC family; it activates the transcription of the structural genes, hupSLC, of the [NiFe]hydrogenase. The lipid (Ni-NTA-DOGA) uses the metal chelator nitrilotriacetic group as the hydrophilic headgroup and contains unsaturated oleyl tails to provide the fluidity necessary for two-dimensional protein crystallization. A projection map of the full-length protein at 18 A resolution was generated by analysing electron microscopy micrographs of negatively stained crystals. The HupR protein appeared to be dimeric and revealed a characteristic "propeller-like" motif. Each monomer forms an L-shaped structure.

Adenovirus 3 penton dodecahedron exhibits structural changes of the base on fibre binding.

It was recently shown that co-expression of adenovirus type 3 (Ad3) penton base and fibre in the baculovirus system produces dodecahedral particles, as does the expression of the penton base alone. The structure of both of these dodecahedral particles, with and without fibre, has been determined by cryoelectron microscopy and 3-dimensional reconstruction techniques to a resolution of 25 and 20 A, respectively. The general form of the penton base resembles that of the base protein in the recent reconstruction of adenovirus type 2. There is a remarkable difference in the penton base structure with and without the fibre. The five small protuberances on the outer surface of each base move away from the 5-fold axis by approximately 15 A when the fibre is present. These protuberances are of relatively low density and most probably represent a flexible loop possibly containing the RGD site involved in integrin binding. The fibre is apparently bound to the outer surface of the penton base, rather than inserted into it. The fibre is flexible and the shaft contains two distinct globular regions 26 A in diameter. The volume of the inner cavity of the dodecahedron is 350 +/- 100 nm3. This small volume precludes the use of the inner cavity to house genetic information for gene therapy; however, the possibility remains of linking the gene to the dodecahedron surface in the hope that it will be internalized with the dodecahedron.

Structure of a neutralizing antibody bound bivalently to human rhinovirus 2.

The structure of a complex between human rhinovirus serotype 2 (HRV2) and the weakly neutralizing monoclonal antibody 8F5 has been determined to 25 A resolution by cryo-electron microscopy and 3-D reconstruction techniques. THe antibody is seen to be bound bivalently across the icosahedral 2-fold axis, despite the very short distance of 60 A between the symmetry-related epitopes. The canyon around the 5-fold axis is not obstructed. Due to extreme flexibility of the hinge region the Fc domains occupy random orientations and are not visible in the reconstruction. The atomic coordinates of Fab-8F5 complexes with a synthetic peptide derived from the viral protein 2 (VP2) epitope were fitted to the structure obtained by cryo-electron microscope techniques. The X-ray structure of HRV2 is not unknown, so that of the closely related HRV1A was placed in the electron microscopic density map. The footprint of 8F5 on the viral surface is largely on VP2, but also covers the VP3 loop centred on residue 3060. C alpha atoms of VP1 and 8F5 come no closer than 10 A. Based on the fit of the X-ray coordinates to the electron microscope data, the synthetic 15mer peptide starts and ends in close proximity to the corresponding amino acids of VP2 on HRV1A. However, the respective loops diverge considerably in their overall spatial disposition. It appears from this study that bivalent binding of an antibody directed against a picornavirus exists for a smaller spanning distance than was previously thought possible. Also bivalent binding does not ensure strong neutralization.

Structure of correctly self-assembled bluetongue virus-like particles.

Bluetongue virus-like particles (VLPs), synthesized by coexpression of VP2, VP3, VP5, and VP7 using recombinant baculoviruses, have been examined by cryoelectron microscopy and image analysis. The 3-D reconstruction of these VLPs reveals an icosahedral structure 86 nm in diameter with essentially the same features as for the native Bluetongue virus (BTV) particle. The VLP is thus shown to contain the four constituent proteins as the native virus particle, with each of the protein positions highly occupied. Since the BTV core-like particle formed by coexpression of VP3 and VP7 lacks five VP7 trimers around each of the five-fold axes, it appears that the presence of the outer capsid proteins VP2 and VP5 is necessary for the adhesion of these VP7 trimers around the five-fold axes. The observed spontaneous formation of complete VLP in the absence of the BTV nonstructural proteins implies that the nonstructural proteins are not necessary for the formation of the double-shelled viral capsid. However, the nonstructural proteins may be involved in different aspects of genome replication and packaging.

Cryoelectron microscopy of macromolecular complexes.

Although there are many macromolecular complexes which play extremely important roles in biology, and despite continued progress in X-ray crystallographic and NMR methods, it is still very difficult to obtain atomic level structural information about such large assemblies. It is now clear that a powerful approach is to combine structural information obtained at different levels. Cryoelectron microscopy of frozen-hydrated samples together with computer based 3-D reconstruction can give structural information at the quaternary level. This can then be combined with atomic level structures of individual components, obtained by X-ray crystallography or NMR to build-up a detailed picture of the overall architecture of the complexes and of the interactions between the components. In our laboratory we are particularly interested in developing the complementarity between the different structural approaches. The aim of this short review is to briefly present our ongoing work using cryoelectron microscopy of vitreous ice-embedded samples as a quantitative tool to investigate the assembly and organization of two important biological structures, namely, microtubules and viruses, in particular the bluetongue virus.

Three-dimensional reconstruction of baculovirus expressed bluetongue virus core-like particles by cryo-electron microscopy.

When the viral proteins VP3 and VP7 of bluetongue virus (BTV) are expressed simultaneously in the baculovirus system, core-like particles form spontaneously. The 3-D structure of these core-like particles, determined from cryo-electron micrographs, reveals an icosahedral structure 72.5 nm in diameter with 200 triangular spikes arranged on a T = 13,I lattice; The five spikes around each of the fivefold axes are absent. This is in contrast to the native BTV core particles which have a complete T = 13,I lattice of 260 spikes. The spikes, attributed to VP7 trimers appear as triangular columns 8.0 nm in height with distinct inner and outer domains. The inner shell of the core-like particles, or subcore-like particle, has a T = 1 lattice composed of 60 copies of VP3. The subcore-like particle is noticeably thicker around the fivefold positions. Pores in the subcore-like particle are situated near each of the local sixfold axes, below each six-membered ring of spikes. These pores could allow the passage of metabolites and RNA to and from the core for RNA transcription during infection. It is possible that the synthetic core-like particles have an incomplete complement of VP7 spikes because the ratio of VP7 to VP3 produced in the dual expression system is less than the 13:1 required for complete core-like particles. Only the VP7 spikes which have the strongest affinity for the VP3 inner core and are involved in maintaining the structural integrity of the core-like particle are incorporated. The BTV core-like particle shows greater morphological similarity to the rotavirus than to the reovirus core particle.

Structure of bluetongue virus particles by cryoelectron microscopy.

The structure of the bluetongue virus (BTV) particle, determined by cryoelectron microscopy and image analysis, reveals a well-ordered outer shell which differs markedly from other known Reoviridae. The inner shell is known to have an icosahedral structure with 260 triangular spikes of VP7 trimers arranged on a T = 13,l lattice. The outer shell is seen to consist of 120 globular regions (possibly VP5), which sit neatly on each of the six-membered rings of VP7 trimers. "Sail"-shaped spikes located above 180 of the VP7 trimers form 60 triskelion-type motifs which cover all but 20 of the VP7 trimers. These spikes are possibly the hemagglutinating protein VP2 which contains a virus neutralization epitope. Thus, VP2 and VP5 together form a continuous layer around the inner shell except for holes on the 5-fold axis.

Low pH deforms the influenza virus envelope.

Influenza virus membrane fusion is induced by low pH, which triggers an irreversible conformational change in the viral haemagglutinin (HA). The result of this change is the extrusion of the HA fusion peptide, after which it may act in the fusion of virus and endosomal membranes. Here we describe electron microscopic observations on low pH-treated virus after negative staining or cryo-electron microscopy of virus in the frozen hydrated state. The results indicate a destabilization of the virus membrane at low pH that can be reversed by returning the pH to neutral.

3-D reconstruction of bluetongue virus tubules using cryoelectron microscopy.

Bluetongue virus (BTV) forms tubules in infected mammalian cells. These tubules are virally encoded entities which can be formed with only one protein, NS1. The NS1 protein does not form a part of virus particles, and its function in viral infection is uncertain. Expression of the NS1 gene in insect cells by recombinant baculovirus yields high amounts of NS1 tubules (ca. 50% of cellular proteins) which are morphologically and immunologically similar to authentic BTV NS1 and can be isolated to about 90% purity. The structure of these synthetic NS1 tubules was investigated by cryoelectron microscopy. NS1 tubules are on average 52.3 nm in diameter and up to 100 nm long. The structure of their helical surface lattice has been determined using computer image processing to a resolution of 40 A. The NS1 protein is about 5.3 nm in diameter and forms a dimer-like structure, so that the tubules are composed of helically coiled ribbons of NS1 "dimers," with 21 or 22 dimers per turn. The surface lattice displays P2 symmetry and forms a one-start helix with a pitch of 9.1 nm. The NS1 tubules exist in two slightly different pH-dependent conformational states.

Activation of recA protein: the pitch of the helical complex with single-stranded DNA.

The complex of recA protein with single-stranded DNA in the presence of ATP is the active species in the three enzymatic activities of recA: the initiation of strand exchange, the hydrolysis of ATP and the cleavage of repressors. Here we find by cryo-electron microscopy of unstained and unfixed samples that the helical structure of the protein coat in this complex differs slightly but significantly from the structure in the complex with double-stranded DNA. We discuss how the larger pitch of the complex with single strands (100 +/- 2 A compared with 95 +/- 2 A with double strands) could contribute to its higher enzymatic activity.

Low resolution structure of the influenza C glycoprotein determined by electron microscopy.

The influenza C glycoprotein is clearly seen to be a trimer in specimens prepared with uranyl stains. Three-dimensional reconstructions from naturally occurring hexagonal arrays show that at low resolution (approximately 30 A) the influenza C glycoprotein exhibits similar features to the haemagglutinin glycoprotein of influenza A. Both have a triangular stalk near the membrane. Further from the membrane, the stalk becomes broader and the monomers more separated, leaving an open centre. The molecule narrows at the top. The regions of greatest contact between adjacent trimers in the arrays are situated nearer the distal end of the molecule. These contact zones can be related to equivalent zones on the influenza A haemagglutinin. Differences between the structure of the influenza A haemagglutinin glycoprotein determined by X-ray analysis and reconstructions of the influenza C glycoprotein are greatest at either end of the molecule, where the reconstructions are least reliable. Ordered glycoprotein arrays have not been observed on influenza C virions incubated at low pH. The staining patterns of glycoproteins on intact virions are essentially determined by the pH at which the virus is incubated, and the stain type, but not the pH of the stain.

Electron microscope structural study of modified fibrin and a related modified fibrinogen aggregate.

The structure of proteolytically modified fibrin and a closely related modified fibrinogen aggregate have been studied by analysis of electron microscope images. For both structures, we propose a model that consists of double-stranded, 2-fold helical protofibrils, which are associated laterally to form ordered fibrils, with a C222 space group: a = 44.0 nm, b = c = 9.4 nm. Each fibril is 80 nm or less in diameter, and twists along its length in a right-handed sense, with a pitch from 7 to 12 times the molecular length. The fibrils associate laterally to form bundles, which tend to twist in a left-handed sense, with a pitch of the order of 40 times the molecular length. The specific volume of modified fibrin calculated from this model is 3.9 A3 per dalton, which is comparable to the specific volume of 3.6 A3 per dalton for modified fibrinogen crystals but is lower than the 6 A3 per dalton determined for fibrin from light-scattering experiments. Comparison of our electron microscope results with X-ray and neutron diffraction data suggest a similar, but less well-ordered, structure for native fibrin, with a smaller fibril, approximately 18.4 nm wide, consisting of eight protofibrils.