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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
Components(Structural polyprotein) x 2
KeywordsVIRUS / icosahedral protein shell / icosahedral virus
Function / homologyFlavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set ...Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Peptidase S3, togavirin / Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Immunoglobulin E-set / Peptidase S1, PA clan / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / membrane fusion / ubiquitin-like protein ligase binding / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / host cell cytoplasm / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / Structural polyprotein
Function and homology information
Specimen sourceSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9 Å resolution
AuthorsLi, L. / Jose, J. / Xiang, Y. / Kuhn, R.J. / Rossmann, M.G.
CitationJournal: Nature / Year: 2010
Title: Structural changes of envelope proteins during alphavirus fusion.
Authors: 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 typeGroupCategoryItemProviderType
1.0Nov 24, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1121
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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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: Protein/peptide
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 / Strain: Toto64
References: UniProt: P03316, Hydrolases, Acting on peptide bonds (peptidases), Serine endopeptidases
#2: Protein/peptide
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 / Strain: Toto64
References: UniProt: P03316, Hydrolases, Acting on peptide bonds (peptidases), Serine endopeptidases

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Experimental details

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Experiment

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

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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 FIELDBright-field microscopy / 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 PROGRAMS3D reconstruction
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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