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- EMDB-31533: Cryo-EM structure of an alphavirus, Getah virus -

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Basic information

Entry
Database: EMDB / ID: EMD-31533
TitleCryo-EM structure of an alphavirus, Getah virus
Map data
Sample
  • Virus: Getah virus
    • Protein or peptide: Envelope glycoprotein 1
    • Protein or peptide: Envelope glycoprotein 2
    • Protein or peptide: capsid proteinCapsid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: STEARIC ACID
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL
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 speciesGetah virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsLiu Z / Liu C / Wang A
Funding support China, 2 items
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, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31533.png

Downloads & links

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Map

FileDownload / File: emd_31533.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-32.610554 - 46.012245
Average (Standard dev.)4.1085538e-10 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 849.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Getah virus

EntireName: Getah virus
Components
  • Virus: Getah virus
    • Protein or peptide: Envelope glycoprotein 1
    • Protein or peptide: Envelope glycoprotein 2
    • Protein or peptide: capsid proteinCapsid
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: STEARIC ACID
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL

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Supramolecule #1: Getah virus

SupramoleculeName: Getah virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 59300 / Sci species name: Getah virus / Sci species strain: GETV-V1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: Envelope glycoprotein 1

MacromoleculeName: Envelope glycoprotein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Getah virus
Molecular weightTheoretical: 47.560648 KDa
SequenceString: YEHTATIPNV VGFPYKAHIE RNGFSPMTLQ LEVLGTSLEP TLNLEYITCE YKTVVPSPYI KCCGTSECRS MERPDYQCQV YTGVYPFMW GGAYCFCDTE NTQLSEAYVD RSDVCKHDHA AAYKAHTAAM KATIRISYGN LNQTTTAFVN GEHTVTVGGS R FTFGPIST ...String:
YEHTATIPNV VGFPYKAHIE RNGFSPMTLQ LEVLGTSLEP TLNLEYITCE YKTVVPSPYI KCCGTSECRS MERPDYQCQV YTGVYPFMW GGAYCFCDTE NTQLSEAYVD RSDVCKHDHA AAYKAHTAAM KATIRISYGN LNQTTTAFVN GEHTVTVGGS R FTFGPIST AWTPFDNKIV VYKNDVYNQD FPPYGSGQPG RFGDIQSRTV ESKDLYANTA LKLSRPSSGT VHVPYTQTPS GF KYWLKER GTSLNDKAPF GCVIKTNPVR AENCAVGNIP VSMDIPDTAF TRVIDAPAVT NLECQVAVCT HSSDFGGIAT LTF KTDKPG KCAVHSHSNV ATIQEAAVDI KTDGKITLHF STASASPAFK VSVCSAKTTC TAACEPPKDH IVPYGASHNN QVFP DMSGT AMTWVQRVAG GLGGLTLAAV AVLILVTCVT MRR

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Macromolecule #2: Envelope glycoprotein 2

MacromoleculeName: Envelope glycoprotein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Getah virus
Molecular weightTheoretical: 46.147492 KDa
SequenceString: SVTEHFNVYK ATKPYLAYCA DCGDGQFCYS PVAIEKIRDE ASDGMIKIQV AAQIGINKGG THEHNKIRYI AGHDMKEANR DSLQVYTSG VCAIRGTMGH FIVAYCPPGD ELKVQFQDAE SHTQACKVQY KHAPAPVGRE KFTVRPHFGI EVPCTTYQLT T APTEEEID ...String:
SVTEHFNVYK ATKPYLAYCA DCGDGQFCYS PVAIEKIRDE ASDGMIKIQV AAQIGINKGG THEHNKIRYI AGHDMKEANR DSLQVYTSG VCAIRGTMGH FIVAYCPPGD ELKVQFQDAE SHTQACKVQY KHAPAPVGRE KFTVRPHFGI EVPCTTYQLT T APTEEEID MHTPPDIPDI TLLSQQSGNV KITAGGKTIR YNCTCGSGNV GTTSSDKTIN SCKIAQCHAA VTNHDKWQYT SS FVPRADQ LSRKGKVHVP FPLTNSTCRV PVARAPGVTY GKRELTVKLH PDHPTLLTYR SLGADPRPYE EWIDRYVERT IPV TEDGIE YRWGNNPPVR LWAQLTTEGK PHGWPHEIIL YYYGLYPAAT IAAVSAAGLA VVLSLLASCY MFATARRKCL TPYA LTPGA VVPVTLGVLC CAPR

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Macromolecule #3: capsid protein

MacromoleculeName: capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO / EC number: togavirin
Source (natural)Organism: Getah virus
Molecular weightTheoretical: 30.200117 KDa
SequenceString: MNYIPTQTFY GRRWRPRPAY RPWRVPMQPA PPMVIPELQT PIVQAQQMQQ LISAVSALTT KQNGKAPKKP KKKPQKAKAK KNEQQKKNE NKKPPPKQKN PAKKKKPGKR ERMCMKIEND CIFEVKLDGK VTGYACLVGD KVMKPAHVKG VIDNPDLAKL T YKKSSKYD ...String:
MNYIPTQTFY GRRWRPRPAY RPWRVPMQPA PPMVIPELQT PIVQAQQMQQ LISAVSALTT KQNGKAPKKP KKKPQKAKAK KNEQQKKNE NKKPPPKQKN PAKKKKPGKR ERMCMKIEND CIFEVKLDGK VTGYACLVGD KVMKPAHVKG VIDNPDLAKL T YKKSSKYD LECAQIPVHM KSDASKYTHE KPEGHYNWHH GAVQYSGGRF TIPTGAGKPG DSGRPIFDNK GRVVAIVLGG AN EGARTAL SVVTWTKDMV TRYTPEGTEE W

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #8: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 8 / Number of copies: 4 / Formula: PCW
Molecular weightTheoretical: 787.121 Da
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Macromolecule #9: STEARIC ACID

MacromoleculeName: STEARIC ACID / type: ligand / ID: 9 / Number of copies: 8 / Formula: STE
Molecular weightTheoretical: 284.477 Da
Chemical component information

ChemComp-STE:
STEARIC ACID / Stearic acid

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Macromolecule #10: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 10 / Number of copies: 12 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Macromolecule #11: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 11 / Number of copies: 12 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: NICKEL/TITANIUM / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00038 kPa
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 16894 / Average electron dose: 1.25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 171059
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Software - details: CTFFIND 4.1 was used to estimate CTF
Startup modelType of model: EMDB MAP
EMDB ID:

31533

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 2041957
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3j0c

chain_id: D

3j0c

chain_id: E

3j0c

chain_id: F
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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