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- PDB-8yvy: Semliki Forest virus virion -

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Basic information

Entry
Database: PDB / ID: 8yvy
TitleSemliki Forest virus virion
Components
  • Spike glycoprotein E1
  • Spike glycoprotein E2
  • Spike glycoprotein E3
  • capsid protein
KeywordsVIRAL PROTEIN / Semliki Forest virus virion / VLDLR
Function / homology:
Function and homology information
Biological speciesSemliki Forest virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsZheng, T. / Wang, J. / Yang, D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Semliki Forest virus viron
Authors: Zheng, T.
History
DepositionMar 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 11, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 16, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein E1
B: Spike glycoprotein E2
C: Spike glycoprotein E3
D: capsid protein
F: Spike glycoprotein E1
G: Spike glycoprotein E1
H: Spike glycoprotein E1
I: Spike glycoprotein E2
J: Spike glycoprotein E2
K: Spike glycoprotein E2
L: Spike glycoprotein E3
M: Spike glycoprotein E3
N: Spike glycoprotein E3
O: capsid protein
P: capsid protein
Q: capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,43328
Polymers470,39516
Non-polymers7,03912
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Spike glycoprotein E1


Mass: 47489.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#2: Protein
Spike glycoprotein E2


Mass: 46468.867 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: Molecular name is based on https://www.ebi.ac.uk/interpro/protein/UniProt/A0A0E3T652/ as Uniprot Reference A0A0E3T652 and author provided name are both Structural polyprotein.
Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#3: Protein
Spike glycoprotein E3


Mass: 5848.729 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#4: Protein
capsid protein


Mass: 17791.299 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus 4 / References: UniProt: A0A0E3T652
#5: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Semliki Forest virus viron / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#4 / Source: NATURAL
Source (natural)Organism: Semliki Forest virus 4
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: C-flat-1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15328 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00834292
ELECTRON MICROSCOPYf_angle_d0.87546704
ELECTRON MICROSCOPYf_dihedral_angle_d6.0994896
ELECTRON MICROSCOPYf_chiral_restr0.0575296
ELECTRON MICROSCOPYf_plane_restr0.0075992

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