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- PDB-3muw: Pseudo-atomic structure of the E2-E1 protein shell in Sindbis virus -

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Basic information

Entry
Database: PDB / ID: 3muw
TitlePseudo-atomic structure of the E2-E1 protein shell in Sindbis virus
DescriptorStructural polyprotein (E.C.3.4.21.-)
KeywordsVIRUS / icosahedral protein shell / icosahedral virus
Specimen sourceSindbis virus / virus / SINV / シンドビスウイルス
MethodElectron microscopy (9 Å resolution / Particle / Single particle)
AuthorsLi, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
CitationNature, 2010, 468, 705-708

Nature, 2010, 468, 705-708 StrPapers
Structural changes of envelope proteins during alphavirus fusion.
Long Li / Joyce Jose / Ye Xiang / Richard J Kuhn / Michael G Rossmann

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 3, 2010 / Release: Nov 24, 2010
RevisionDateData content typeGroupProviderType
1.0Nov 24, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

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  • 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-1121
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Assembly

Deposited unit
A: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein


Theoretical massNumber of molelcules
Total (without water)319,2828
Polyers319,2828
Non-polymers00
Water0
#1
A: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)19,156,897480
Polyers19,156,897480
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: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein
x 5


  • icosahedral pentamer
  • 1.6 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,596,40840
Polyers1,596,40840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Structural polyprotein
U: Structural polyprotein
D: Structural polyprotein
X: Structural polyprotein
E: Structural polyprotein
Y: Structural polyprotein
F: Structural polyprotein
Z: Structural polyprotein
x 6


  • icosahedral 23 hexamer
  • 1.92 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)1,915,69048
Polyers1,915,69048
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)
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 envelope glycoprotein / Spike glycoprotein E2 / 6K protein / E1 envelope glycoprotein / Spike glycoprotein E1 / Coordinate model: Cα atoms only


Mass: 41311.758 Da / Num. of mol.: 4
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316, EC: 3.4.21.-

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 envelope glycoprotein / Spike glycoprotein E2 / 6K protein / E1 envelope glycoprotein / Spike glycoprotein E1 / Coordinate model: Cα atoms only


Mass: 38508.645 Da / Num. of mol.: 4
Source: (natural) Sindbis virus / virus / シンドビスウイルス
References: UniProt: P03316, EC: 3.4.21.-

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

Component
IDNameTypeParent ID
1Sindbis virusVIRUS0
2E2-E1 protein shell of Sindbis virus1
Details of virusVirus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: TNE buffer / Details: TNE buffer / pH: 7.5
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: This grid plus sample was kept at 100 K
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200T / Date: Jun 21, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 / Calibrated magnification: 39220 / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 18 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1EMFitMODEL FITTING
2PURDUE PROGRAMSRECONSTRUCTION
CTF correctionDetails: CTF correction of each particle.
SymmetryPoint symmetry: I
3D reconstructionMethod: model-based common lines / Resolution: 9 Å / Number of particles: 7085 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: sumf
Atomic model buildingPDB-ID: 3MUU
Number of atoms included #LASTProtein: 2468 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 2468

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