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- PDB-3j0f: Sindbis virion -

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Basic information

Entry
Database: PDB / ID: 3j0f
TitleSindbis virion
DescriptorCapsid protein
E1 envelope glycoprotein
E2 envelope glycoprotein
KeywordsVIRUS / alphavirus / virus assembly / glycoprotein
Specimen sourceSindbis virus / virus / SINV / シンドビスウイルス
MethodElectron microscopy (7 Å resolution / Particle / Single particle)
AuthorsTang, J. / Jose, J. / Zhang, W. / Chipman, P. / Kuhn, R.J. / Baker, T.S.
CitationJ. Mol. Biol., 2011, 414, 442-459

J. Mol. Biol., 2011, 414, 442-459 StrPapers
Molecular links between the E2 envelope glycoprotein and nucleocapsid core in Sindbis virus.
Jinghua Tang / Joyce Jose / Paul Chipman / Wei Zhang / Richard J Kuhn / Timothy S Baker

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 8, 2011 / Release: Oct 12, 2011
RevisionDateData content typeGroupProviderType
1.0Oct 12, 2011Structure modelrepositoryInitial release
1.1Nov 9, 2011Structure modelDatabase references
1.2Dec 21, 2011Structure modelDatabase references
1.3May 30, 2012Structure modelRefinement description

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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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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
Polyers495,23812
Non-polymers00
Water0
#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
Polyers29,714,263720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#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
Polyers2,476,18960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#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
Polyers2,971,42672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)
Capsid protein / Coat protein / C / Coordinate model: Cα atoms only


Mass: 29410.010 Da / Num. of mol.: 4 / Fragment: UNP residues 1-264
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316, EC: 3.4.21.90

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
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: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

#3: Polypeptide(L)
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: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316

Cellular component

Molecular function

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: sindbis virion / Type: VIRUS / Details: alphavirus
Details of virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus 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

MicroscopyMicroscope model: 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 deg. / Tilt angle min: 0 deg.
Image recordingFilm or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SymmetryPoint symmetry: I
3D reconstructionResolution: 7 Å / Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model buildingPDB-ID: 1KXF
Pdb chain ID: A
Number of atoms included #LASTProtein: 4064 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 4064

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