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- PDB-7v4t: Cryo-EM structure of Alphavirus M1 -

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Basic information

Entry
Database: PDB / ID: 7v4t
TitleCryo-EM structure of Alphavirus M1
Components
  • Capsid proteinCapsid
  • E1 glycoprotein
  • E2 glycoprotein
KeywordsVIRUS / Alphavirus M1
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / 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 ...T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / 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
Alphavirus E2 glycoprotein, domain B / 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 E2 glycoprotein, domain B / 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 / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesAlphavirus M1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsGao, Y. / Jia, X. / Zhang, Q.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81973342 China
National Natural Science Foundation of China (NSFC)81773751 China
National Natural Science Foundation of China (NSFC)81772675 China
National Natural Science Foundation of China (NSFC)81903652 China
National Natural Science Foundation of China (NSFC)81802536 China
CitationJournal: To Be Published
Title: Cryo-EM evidence of viral N-glycosylation reveal receptor binding mechanisms of alphavirus M1
Authors: Song, D. / Jia, X.
History
DepositionAug 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
I: E1 glycoprotein
J: E2 glycoprotein
K: Capsid protein
M: E1 glycoprotein
N: E2 glycoprotein
O: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)499,22624
Polymers496,57112
Non-polymers2,65412
Water0
1
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
I: E1 glycoprotein
J: E2 glycoprotein
K: Capsid protein
M: E1 glycoprotein
N: E2 glycoprotein
O: Capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)29,953,5381440
Polymers29,794,268720
Non-polymers159,270720
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
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
I: E1 glycoprotein
J: E2 glycoprotein
K: Capsid protein
M: E1 glycoprotein
N: E2 glycoprotein
O: Capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 2.5 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,496,128120
Polymers2,482,85660
Non-polymers13,27260
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: E1 glycoprotein
B: E2 glycoprotein
C: Capsid protein
E: E1 glycoprotein
F: E2 glycoprotein
G: Capsid protein
I: E1 glycoprotein
J: E2 glycoprotein
K: Capsid protein
M: E1 glycoprotein
N: E2 glycoprotein
O: Capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)2,995,354144
Polymers2,979,42772
Non-polymers15,92772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
E1 glycoprotein


Mass: 47595.766 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alphavirus M1 / References: UniProt: A0MNM2
#2: Protein
E2 glycoprotein


Mass: 46462.031 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alphavirus M1 / References: UniProt: A0MNM2
#3: Protein
Capsid protein / Capsid


Mass: 30084.988 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Alphavirus M1 / References: UniProt: A0MNM2
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY

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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: Alphavirus M1 / Type: VIRUS / Entity ID: #1-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Alphavirus M1
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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 FIELDBright-field microscopy
Image recordingElectron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameCategory
2SerialEMimage acquisition
4GctfCTF correction
10RELIONinitial Euler assignment
11jsprfinal Euler assignment
13jspr3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 32894 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00332300
ELECTRON MICROSCOPYf_angle_d0.7143988
ELECTRON MICROSCOPYf_dihedral_angle_d5.4684508
ELECTRON MICROSCOPYf_chiral_restr0.0484956
ELECTRON MICROSCOPYf_plane_restr0.0065656

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