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- PDB-7fd2: Cryo-EM structure of an alphavirus, Getah virus -

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Basic information

Entry
Database: PDB / ID: 7fd2
TitleCryo-EM structure of an alphavirus, Getah virus
Components
  • (Envelope glycoprotein ...) x 2
  • capsid proteinCapsid
KeywordsVIRUS / mature / Infective
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
CHOLESTEROL / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / PALMITIC ACID / STEARIC ACID / Structural polyprotein
Similarity search - Component
Biological speciesGetah virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsLiu, Z. / Liu, C. / Wang, A.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81870246 China
National Natural Science Foundation of China (NSFC)82070329 China
CitationJournal: Cell Discov / Year: 2022
Title: Structure of infective Getah virus at 2.8 Å resolution determined by cryo-electron microscopy.
Authors: Aojie Wang / Feng Zhou / Congcong Liu / Dongsheng Gao / Ruxi Qi / Yiheng Yin / Sheng Liu / Yuanzhu Gao / Lutang Fu / Yinhe Xia / Yawei Xu / Chuanqing Wang / Zheng Liu /
Abstract: Getah virus (GETV), a member of the genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% ...Getah virus (GETV), a member of the genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% of healthy people, there are no reports of clinical symptoms associated with GETV. The biological and pathological properties of GETV are largely unknown and antiviral or vaccine treatments against GETV are still unavailable due to a lack of knowledge of the structure of the GETV virion. Here, we present the structure of infective GETV at a resolution of 2.8 Å with the atomic models of the capsid protein and the envelope glycoproteins E1 and E2. We have identified numerous glycosylation and S-acylation sites in E1 and E2. The surface-exposed glycans indicate a possible impact on viral immune evasion and host cell invasion. The S-acylation sites might be involved in stabilizing the transmembrane assembly of E1 and E2. In addition, a cholesterol and a phospholipid molecule are observed in a transmembrane hydrophobic pocket, together with two more cholesterols surrounding the pocket. The cholesterol and phospholipid stabilize the hydrophobic pocket in the viral envelope membrane. The structural information will assist structure-based antiviral and vaccine screening, design, and optimization.
History
DepositionJul 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Envelope glycoprotein 1
B: Envelope glycoprotein 2
C: capsid protein
E: Envelope glycoprotein 1
F: Envelope glycoprotein 2
G: capsid protein
I: Envelope glycoprotein 1
J: Envelope glycoprotein 2
K: capsid protein
M: Envelope glycoprotein 1
N: Envelope glycoprotein 2
O: capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)516,69864
Polymers495,63312
Non-polymers21,06552
Water0
1
A: Envelope glycoprotein 1
B: Envelope glycoprotein 2
C: capsid protein
E: Envelope glycoprotein 1
F: Envelope glycoprotein 2
G: capsid protein
I: Envelope glycoprotein 1
J: Envelope glycoprotein 2
K: capsid protein
M: Envelope glycoprotein 1
N: Envelope glycoprotein 2
O: capsid protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)31,001,8563840
Polymers29,737,982720
Non-polymers1,263,8743120
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: Envelope glycoprotein 1
B: Envelope glycoprotein 2
C: capsid protein
E: Envelope glycoprotein 1
F: Envelope glycoprotein 2
G: capsid protein
I: Envelope glycoprotein 1
J: Envelope glycoprotein 2
K: capsid protein
M: Envelope glycoprotein 1
N: Envelope glycoprotein 2
O: capsid protein
hetero molecules
x 5


  • icosahedral pentamer
  • 2.58 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,583,488320
Polymers2,478,16560
Non-polymers105,323260
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Envelope glycoprotein 1
B: Envelope glycoprotein 2
C: capsid protein
E: Envelope glycoprotein 1
F: Envelope glycoprotein 2
G: capsid protein
I: Envelope glycoprotein 1
J: Envelope glycoprotein 2
K: capsid protein
M: Envelope glycoprotein 1
N: Envelope glycoprotein 2
O: capsid protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 3.1 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)3,100,186384
Polymers2,973,79872
Non-polymers126,387312
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

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Envelope glycoprotein ... , 2 types, 8 molecules AEIMBFJN

#1: Protein
Envelope glycoprotein 1


Mass: 47560.648 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Getah virus / References: UniProt: A0A1Z2R994, togavirin
#2: Protein
Envelope glycoprotein 2 / p130


Mass: 46147.492 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Getah virus / References: UniProt: A0A1Z2R994, togavirin

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Protein , 1 types, 4 molecules CGKO

#3: Protein
capsid protein / Capsid


Mass: 30200.117 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Getah virus / References: UniProt: A0A1Z2R994, togavirin

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Sugars , 4 types, 16 molecules

#4: Polysaccharide
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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.: 4 / 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

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Non-polymers , 4 types, 36 molecules

#8: Chemical
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H85NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPC, phospholipid*YM
#9: Chemical
ChemComp-STE / STEARIC ACID / Stearic acid


Mass: 284.477 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C18H36O2 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical
ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION

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Details

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: Getah virus / Type: VIRUS / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Getah virus / Strain: GETV-V1
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: NICKEL/TITANIUM / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/2
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 FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 1500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16894
Image scansWidth: 5760 / Height: 4092

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategoryDetails
2RELION3.0.8image acquisitionRelion3.0.8 was used to Class3d, Refine3D, postprocess and polishing
3jspr2017image acquisitionJSPR was used to align particles and crop particles
5CTFFIND4.1CTF correctionCTFFIND 4.1 was used to estimate CTF
8UCSF Chimera1.13.1model fitting
10PHENIX1.18.2model refinement
11RELION3.0.8initial Euler assignment
12RELION3.0.8final Euler assignment
13RELION3.0.8classification
14RELION3.0.83D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 171059
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2041957 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-ID
13J0C

3j0c

D1
23J0C

3j0c

E1
33J0C

3j0c

F1
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00533424
ELECTRON MICROSCOPYf_angle_d1.04445429
ELECTRON MICROSCOPYf_dihedral_angle_d9.7995064
ELECTRON MICROSCOPYf_chiral_restr0.0615187
ELECTRON MICROSCOPYf_plane_restr0.0175675

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