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- PDB-3j0f: Sindbis virion -

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Basic information

Entry
Database: PDB / ID: 3j0f
TitleSindbis virion
Components
  • Capsid protein
  • E1 envelope glycoprotein
  • E2 envelope glycoprotein
KeywordsVIRUS / alphavirus / virus assembly / glycoprotein
Function / homology
Function and homology information


icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / viral translational frameshifting / serine-type endopeptidase activity ...icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / 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
Similarity search - Component
Biological speciesSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsTang, J. / Jose, J. / Zhang, W. / Chipman, P. / Kuhn, R.J. / Baker, T.S.
CitationJournal: J Mol Biol / Year: 2011
Title: Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.
Authors: Jinghua Tang / Joyce Jose / Paul Chipman / Wei Zhang / Richard J Kuhn / Timothy S Baker /
Abstract: A three-dimensional reconstruction of Sindbis virus at 7.0 Å resolution presented here provides a detailed view of the virion structure and includes structural evidence for key interactions that ...A three-dimensional reconstruction of Sindbis virus at 7.0 Å resolution presented here provides a detailed view of the virion structure and includes structural evidence for key interactions that occur between the capsid protein (CP) and transmembrane (TM) glycoproteins E1 and E2. Based on crystal structures of component proteins and homology modeling, we constructed a nearly complete, pseudo-atomic model of the virus. Notably, this includes identification of the 33-residue cytoplasmic domain of E2 (cdE2), which follows a path from the E2 TM helix to the CP where it enters and exits the CP hydrophobic pocket and then folds back to contact the viral membrane. Modeling analysis identified three major contact regions between cdE2 and CP, and the roles of specific residues were probed by molecular genetics. This identified R393 and E395 of cdE2 and Y162 and K252 of CP as critical for virus assembly. The N-termini of the CPs form a contiguous network that interconnects 12 pentameric and 30 hexameric CP capsomers. A single glycoprotein spike cross-links three neighboring CP capsomers as might occur during initiation of virus budding.
History
DepositionJul 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3May 30, 2012Group: Refinement description
Revision 1.4Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / em_image_scans / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5251
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein


Theoretical massNumber of molelcules
Total (without water)495,23812
Polymers495,23812
Non-polymers00
Water00
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein
x 60


Theoretical massNumber of molelcules
Total (without water)29,714,263720
Polymers29,714,263720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein
x 5


  • icosahedral pentamer
  • 2.48 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,476,18960
Polymers2,476,18960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
D: Capsid protein
E: E1 envelope glycoprotein
F: E1 envelope glycoprotein
G: E1 envelope glycoprotein
H: E1 envelope glycoprotein
I: E2 envelope glycoprotein
J: E2 envelope glycoprotein
K: E2 envelope glycoprotein
L: E2 envelope glycoprotein
x 6


  • icosahedral 23 hexamer
  • 2.97 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,971,42672
Polymers2,971,42672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Capsid protein / Coat protein / C / Coordinate model: Cα atoms only


Mass: 29410.010 Da / Num. of mol.: 4 / Fragment: UNP residues 1-264 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / References: UniProt: P03316, togavirin
#2: Protein
E1 envelope glycoprotein / Spike glycoprotein E1 / Coordinate model: Cα atoms only


Mass: 47416.836 Da / Num. of mol.: 4 / Fragment: UNP residues 807-1245 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / References: UniProt: P03316
#3: Protein
E2 envelope glycoprotein / Spike glycoprotein E2 / Coordinate model: Cα atoms only


Mass: 46982.582 Da / Num. of mol.: 4 / Fragment: UNP residues 329-751 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / References: UniProt: P03316

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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: sindbis virion / Type: VIRUS / Details: alphavirus
Details of virusEmpty: NO / Enveloped: YES / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Dec 12, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: eucentric / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 7 Å / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 1KXF

1kxf


Pdb chain-ID: A / Accession code: 1KXF / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 0 0 4064

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