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- EMDB-31951: Cryo-EM structure of Vaccinia virus scaffolding protein D13 with ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31951 | ||||||||||||
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Title | Cryo-EM structure of Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation | ||||||||||||
![]() | Cryo-EM single particle reconstruction on Vaccinia virus scaffold protein D13 trimer (N-terminal 17-residue truncation mutant). The map has been sharpened and density-normalized. | ||||||||||||
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![]() | Scaffold / capsid / double-jelly-roll / VIRAL PROTEIN | ||||||||||||
Function / homology | Poxvirus rifampicin-resistance / Poxvirus rifampicin resistance protein / response to antibiotic / identical protein binding / membrane / Scaffold protein OPG125![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||
![]() | Wolf M / Hyun J | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Assembly mechanism of the pleomorphic immature poxvirus scaffold. Authors: Jaekyung Hyun / Hideyuki Matsunami / Tae Gyun Kim / Matthias Wolf / ![]() ![]() ![]() Abstract: In Vaccinia virus (VACV), the prototype poxvirus, scaffold protein D13 forms a honeycomb-like lattice on the viral membrane that results in formation of the pleomorphic immature virion (IV). The ...In Vaccinia virus (VACV), the prototype poxvirus, scaffold protein D13 forms a honeycomb-like lattice on the viral membrane that results in formation of the pleomorphic immature virion (IV). The structure of D13 is similar to those of major capsid proteins that readily form icosahedral capsids in nucleocytoplasmic large DNA viruses (NCLDVs). However, the detailed assembly mechanism of the nonicosahedral poxvirus scaffold has never been understood. Here we show the cryo-EM structures of the D13 trimer and scaffold intermediates produced in vitro. The structures reveal that the displacement of the short N-terminal α-helix is critical for initiation of D13 self-assembly. The continuous curvature of the IV is mediated by electrostatic interactions that induce torsion between trimers. The assembly mechanism explains the semiordered capsid-like arrangement of D13 that is distinct from icosahedral NCLDVs. Our structures explain how a single protein can self-assemble into different capsid morphologies and represent a local exception to the universal Caspar-Klug theory of quasi-equivalence. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25 KB 25 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 103.1 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() ![]() | 5.8 MB 49.4 MB 49.6 MB 49.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vffMC ![]() 7vfdC ![]() 7vfeC ![]() 7vfgC ![]() 7vfhC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Cryo-EM single particle reconstruction on Vaccinia virus scaffold protein D13 trimer (N-terminal 17-residue truncation mutant). The map has been sharpened and density-normalized. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM single particle reconstruction on Vaccinia virus scaffold...
File | emd_31951_additional_1.map | ||||||||||||
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Annotation | Cryo-EM single particle reconstruction on Vaccinia virus scaffold protein D13 trimer (N-terminal 17-residue truncation mutant). The map has been density-modified and density-normalized. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Cryo-EM single particle reconstruction on Vaccinia virus scaffold...
File | emd_31951_additional_2.map | ||||||||||||
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Annotation | Cryo-EM single particle reconstruction on Vaccinia virus scaffold protein D13 trimer (N-terminal 17-residue truncation mutant). The map is unsharpened and density-normalized. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM single particle reconstruction on Vaccinia virus scaffold...
File | emd_31951_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM single particle reconstruction on Vaccinia virus scaffold protein D13 trimer (N-terminal 17-residue truncation mutant, half map 1). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM single particle reconstruction on Vaccinia virus scaffold...
File | emd_31951_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM single particle reconstruction on Vaccinia virus scaffold protein D13 trimer (N-terminal 17-residue truncation mutant, half map 2). | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Vaccinia virus scaffolding protein D13 with N-terminal 17 residue...
Entire | Name: Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation in its trimeric state |
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Components |
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-Supramolecule #1: Vaccinia virus scaffolding protein D13 with N-terminal 17 residue...
Supramolecule | Name: Vaccinia virus scaffolding protein D13 with N-terminal 17 residue truncation in its trimeric state type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Recombinant D13 was expressed with N-terminal polyhistidine-tag (His-tag) using bacterial expression system. The protein was purified using metal affinity chromatography. His-tag was removed ...Details: Recombinant D13 was expressed with N-terminal polyhistidine-tag (His-tag) using bacterial expression system. The protein was purified using metal affinity chromatography. His-tag was removed by proteolysis and the protein was further purified using size exclusion chromatography. The final purified protein was trimeric. |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 180 KDa |
-Macromolecule #1: Scaffold protein D13
Macromolecule | Name: Scaffold protein D13 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 59.817219 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: RSNVFAVDSQ IPTLYMPQYI SLSGVMTNDG PDNQAIASFE IRDQYITALN HLVLSLELPE VKGMGRFGYV PYVGYKCINH VSISSCNGV IWEIEGEELY NNCINNTIAL KHSGYSSELN DISIGLTPND TIKEPSTVYV YIKTPFDVED TFSSLKLSDS K ITVTVTFN ...String: RSNVFAVDSQ IPTLYMPQYI SLSGVMTNDG PDNQAIASFE IRDQYITALN HLVLSLELPE VKGMGRFGYV PYVGYKCINH VSISSCNGV IWEIEGEELY NNCINNTIAL KHSGYSSELN DISIGLTPND TIKEPSTVYV YIKTPFDVED TFSSLKLSDS K ITVTVTFN PVSDIVIRDS SFDFETFNKE FVYVPELSFI GYMVKNVQIK PSFIEKPRRV IGQINQPTAT VTEVHAATSL SV YTKPYYG NTDNKFISYP GYSQDEKDYI DAYVSRLLDD LVIVSDGPPT GYPESAEIVE VPEDGIVSIQ DADVYVKIDN VPD NMSVYL HTNLLMFGTR KNSFIYNISK KFSAITGTYS DATKRTIFAH ISHSINIIDT SIPVSLWTSQ RNVYNGDNRS AESK AKDLF INDPFIKGID FKNKTDIISR LEVRFGNDVL YSENGPISRI YNELLTKSNN GTRTLTFNFT PKIFFRPTTI TANVS RGKD KLSVRVVYST MDVNHPIYYV QKQLVVVCND LYKVSYDQGV SITKIMG UniProtKB: Scaffold protein OPG125 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.12 mg/mL | ||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 3 microliter sample volume was loaded onto a holey grid with additional graphene oxide film. 10 sec waiting time, 5 sec blotting time and blot force 0, no delay time were applied before plunging.. |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 1227 / Average exposure time: 83.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 92000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |