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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 / homology
Function and homology information


icosahedral viral capsid, spike / togavirin / membrane fusion / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell cytoplasm ...icosahedral viral capsid, spike / togavirin / membrane fusion / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell cytoplasm / host cell nucleus / serine-type endopeptidase activity / host cell plasma membrane / virion membrane / structural molecule activity / RNA binding / integral component of membrane
Similarity search - Function
Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, domain B / Alphavirus E2 glycoprotein, domain A / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein ...Alphavirus core protein (CP) domain profile. / Alphavirus E1 glycoprotein / Alphavirus E3 glycoprotein / Alphavirus core protein / Alphavirus E2 glycoprotein / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, domain B / Alphavirus E2 glycoprotein, domain A / Alphavirus E1 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E2 glycoprotein / Peptidase S3, togavirin / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / 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: 9 Å
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 /
Abstract: Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope ...Alphaviruses are enveloped RNA viruses that have a diameter of about 700 Å and can be lethal human pathogens. Entry of virus into host cells by endocytosis is controlled by two envelope glycoproteins, E1 and E2. The E2-E1 heterodimers form 80 trimeric spikes on the icosahedral virus surface, 60 with quasi-three-fold symmetry and 20 coincident with the icosahedral three-fold axes arranged with T = 4 quasi-symmetry. The E1 glycoprotein has a hydrophobic fusion loop at one end and is responsible for membrane fusion. The E2 protein is responsible for receptor binding and protects the fusion loop at neutral pH. The lower pH in the endosome induces the virions to undergo an irreversible conformational change in which E2 and E1 dissociate and E1 forms homotrimers, triggering fusion of the viral membrane with the endosomal membrane and then releasing the viral genome into the cytoplasm. Here we report the structure of an alphavirus spike, crystallized at low pH, representing an intermediate in the fusion process and clarifying the maturation process. The trimer of E2-E1 in the crystal structure is similar to the spikes in the neutral pH virus except that the E2 middle region is disordered, exposing the fusion loop. The amino- and carboxy-terminal domains of E2 each form immunoglobulin-like folds, consistent with the receptor attachment properties of E2.
History
DepositionMay 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.angle_alpha / _cell.angle_beta / _cell.angle_gamma / _cell.length_a / _cell.length_b / _cell.length_c

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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-1121
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  • Superimposition on EM map
  • EMDB-1121
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Structure viewerMolecule:
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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
Polymers319,2828
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
Polymers19,156,897480
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
Polymers1,596,40840
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
Polymers1,915,69048
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
SymmetryPoint symmetry: (Schoenflies symbol: I (正20面体型対称))

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Components

#1: Protein
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 ...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 method: isolated from a natural source / Source: (natural) Sindbis virus / Strain: Toto64
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein
Structural polyprotein / p130 / Capsid protein / Coat protein / C / p62 / E3/E2 / E3 protein / Spike glycoprotein E3 / E2 ...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 method: isolated from a natural source / 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 / 3D 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 virusHost category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: TNE buffer / pH: 7.5 / Details: TNE buffer
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

MicroscopyModel: 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 X / Calibrated magnification: 39220 X / Nominal defocus max: 2580 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
Specimen holderTilt angle max: 0 ° / Tilt angle min: 0 °
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 (正20面体型対称)
3D reconstructionMethod: model-based common lines / Resolution: 9 Å / Num. of particles: 7085 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: sumf / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 3MUU
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 0 2468

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