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

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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
Specimen sourceSindbis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 23, 2018 / Release: Mar 13, 2019

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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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
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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
Polyers391,40512
Non-polymers2541
Water0
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
Polyers23,484,327720
Non-polymers15,27060
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
Polyers1,957,02760
Non-polymers1,2725
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers2,348,43372
Non-polymers1,5276
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
Spike glycoprotein E1


Mass: 47186.434 Da / Num. of mol.: 4 / Source: (natural) Sindbis virus
#2: Protein/peptide
Spike glycoprotein E2


Mass: 43184.387 Da / Num. of mol.: 4 / Source: (natural) Sindbis virus
#3: Protein/peptide
Assembly protein E3


Mass: 7480.542 Da / Num. of mol.: 4 / Source: (natural) Sindbis virus
#4: Chemical ChemComp-8K6 / Octadecane / N-Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Formula: C18H38 / Octadecane

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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

ComponentName: Sindbis virus / Type: VIRUS / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Sindbis virus
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus 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
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
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 / Number of particles: 29974 / Symmetry type: POINT

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