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- PDB-9kqr: Cryo-EM Structure of Mature Semliki Forest Virus -

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Basic information

Entry
Database: PDB / ID: 9kqr
TitleCryo-EM Structure of Mature Semliki Forest Virus
Components
  • Capsid protein
  • Envelope glycoprotein E2
  • Spike glycoprotein E1
KeywordsVIRAL PROTEIN / alphavirus / Semliki Forest Virus
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein / Frameshifted structural polyprotein
Similarity search - Component
Biological speciesSemliki Forest virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsJia, X. / Li, S. / Zhang, Q. / He, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2021B1212040017 China
CitationJournal: Dian Zi Xian Wei Xue Bao / Year: 2025
Title: Structural study of Semliki Forest virus through Cryo-EM
Authors: Jia, X. / Li, S. / Yu, H. / Zhang, Q. / He, J.
History
DepositionNov 26, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
k: Envelope glycoprotein E2
l: Capsid protein
j: Spike glycoprotein E1
b: Envelope glycoprotein E2
c: Capsid protein
a: Spike glycoprotein E1
e: Envelope glycoprotein E2
f: Capsid protein
d: Spike glycoprotein E1
h: Envelope glycoprotein E2
i: Capsid protein
g: Spike glycoprotein E1


Theoretical massNumber of molelcules
Total (without water)497,11912
Polymers497,11912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Envelope glycoprotein E2 / Spike glycoprotein E2


Mass: 46870.211 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus / References: UniProt: P0DJZ6
#2: Protein
Capsid protein / Coat protein / C


Mass: 29920.711 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus / References: UniProt: P0DJZ6, togavirin
#3: Protein
Spike glycoprotein E1 / E1 envelope glycoprotein


Mass: 47488.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Semliki Forest virus / References: UniProt: P03315
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 / Type: VIRUS
Details: Mature Semliki Forest Virus Voron isolated from infected Vero cell
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Semliki Forest virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 739620 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 111.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002632260
ELECTRON MICROSCOPYf_angle_d0.550443936
ELECTRON MICROSCOPYf_chiral_restr0.04314880
ELECTRON MICROSCOPYf_plane_restr0.00445684
ELECTRON MICROSCOPYf_dihedral_angle_d5.63984416

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