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- PDB-6imm: Cryo-EM structure of an alphavirus, Sindbis virus -

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Basic information

Entry
Database: PDB / ID: 6imm
TitleCryo-EM structure of an alphavirus, Sindbis virus
Components
  • Assembly protein E3
  • Spike glycoprotein E1
  • Spike glycoprotein E2
KeywordsVIRUS / Alphavirus / Sindbis virus / Glycoprotein
Function / homology
Function and homology information


viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis ...viral capsid / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / plasma membrane / cytoplasm
Similarity search - Function
Helix Hairpins - #2230 / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, A domain / Immunoglobulin-like - #350 / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C ...Helix Hairpins - #2230 / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein, A domain / Immunoglobulin-like - #350 / 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 / Helix Hairpins / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Octadecane / Structural polyprotein
Similarity search - Component
Biological speciesSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, X. / Ma, J. / Chen, L.
CitationJournal: Nat Commun / Year: 2018
Title: Implication for alphavirus host-cell entry and assembly indicated by a 3.5Å resolution cryo-EM structure.
Authors: Lihong Chen / Ming Wang / Dongjie Zhu / Zhenzhao Sun / Jun Ma / Jinglin Wang / Lingfei Kong / Shida Wang / Zaisi Liu / Lili Wei / Yuwen He / Jingfei Wang / Xinzheng Zhang /
Abstract: Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. ...Alphaviruses are enveloped RNA viruses that contain several human pathogens. Due to intrinsic heterogeneity of alphavirus particles, a high resolution structure of the virion is currently lacking. Here we provide a 3.5 Å cryo-EM structure of Sindbis virus, using block based reconstruction method that overcomes the heterogeneity problem. Our structural analysis identifies a number of conserved residues that play pivotal roles in the virus life cycle. We identify a hydrophobic pocket in the subdomain D of E2 protein that is stabilized by an unknown pocket factor near the viral membrane. Residues in the pocket are conserved in different alphaviruses. The pocket strengthens the interactions of the E1/E2 heterodimer and may facilitate virus assembly. Our study provides structural insights into alphaviruses that may inform the design of drugs and vaccines.
History
DepositionOct 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _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-9693
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
N: Spike glycoprotein E1
P: Spike glycoprotein E2
R: Assembly protein E3
T: Spike glycoprotein E1
V: Spike glycoprotein E2
X: Assembly protein E3
Z: Spike glycoprotein E1
a: Spike glycoprotein E1
d: Spike glycoprotein E2
e: Spike glycoprotein E2
h: Assembly protein E3
i: Assembly protein E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)391,66013
Polymers391,40512
Non-polymers2541
Water00
1
N: Spike glycoprotein E1
P: Spike glycoprotein E2
R: Assembly protein E3
T: Spike glycoprotein E1
V: Spike glycoprotein E2
X: Assembly protein E3
Z: Spike glycoprotein E1
a: Spike glycoprotein E1
d: Spike glycoprotein E2
e: Spike glycoprotein E2
h: Assembly protein E3
i: Assembly protein E3
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)23,499,597780
Polymers23,484,327720
Non-polymers15,27060
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
N: Spike glycoprotein E1
P: Spike glycoprotein E2
R: Assembly protein E3
T: Spike glycoprotein E1
V: Spike glycoprotein E2
X: Assembly protein E3
Z: Spike glycoprotein E1
a: Spike glycoprotein E1
d: Spike glycoprotein E2
e: Spike glycoprotein E2
h: Assembly protein E3
i: Assembly protein E3
hetero molecules
x 5


  • icosahedral pentamer
  • 1.96 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,958,30065
Polymers1,957,02760
Non-polymers1,2725
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
N: Spike glycoprotein E1
P: Spike glycoprotein E2
R: Assembly protein E3
T: Spike glycoprotein E1
V: Spike glycoprotein E2
X: Assembly protein E3
Z: Spike glycoprotein E1
a: Spike glycoprotein E1
d: Spike glycoprotein E2
e: Spike glycoprotein E2
h: Assembly protein E3
i: Assembly protein E3
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 2.35 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,349,96078
Polymers2,348,43372
Non-polymers1,5276
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
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 (icosahedral))

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Components

#1: Protein
Spike glycoprotein E1


Mass: 47186.434 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / References: UniProt: A0A3G2BZ29*PLUS
#2: Protein
Spike glycoprotein E2


Mass: 43184.387 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / References: UniProt: A0A3G2BZ29*PLUS
#3: Protein
Assembly protein E3


Mass: 7480.542 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sindbis virus / References: UniProt: A0A3G2BZ29*PLUS
#4: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
Has protein modificationY

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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 virus / Type: VIRUS / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Sindbis virus
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29974 / Symmetry type: POINT

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