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- EMDB-31716: Cryo-EM structure of Alphavirus M1 -

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Basic information

Entry
Database: EMDB / ID: EMD-31716
TitleCryo-EM structure of Alphavirus M1
Map dataCryo-EM structure of alphavirus M1
Sample
  • Virus: Alphavirus M1
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAlphavirus M1 / VIRUS
Function / homology
Function and homology information


T=4 icosahedral viral capsid / host cell cytoplasm / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / membrane
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
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsGao Y / Jia X
Funding support China, 5 items
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, 2021-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31716.png

Downloads & links

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Map

FileDownload / File: emd_31716.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of alphavirus M1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 540 pix.
= 705.78 Å		1.31 Å/pix.
x 540 pix.
= 705.78 Å		1.31 Å/pix.
x 540 pix.
= 705.78 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.307 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-8.154184000000001 - 14.300132
Average (Standard dev.)-0.000000001117083 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-270-270-270
Dimensions540540540
Spacing540540540
CellA=B=C: 705.78 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Alphavirus M1

EntireName: Alphavirus M1
Components
  • Virus: Alphavirus M1
    • Protein or peptide: E1 glycoprotein
    • Protein or peptide: E2 glycoprotein
    • Protein or peptide: Capsid protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Alphavirus M1

SupramoleculeName: Alphavirus M1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 97469 / Sci species name: Alphavirus M1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: E1 glycoprotein

MacromoleculeName: E1 glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Alphavirus M1
Molecular weightTheoretical: 47.595766 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 VYKNDVYNLD FPPYGSGQPG RFGDIQSRTV ESKDLYANTA LKLSRPSSGT VHVPYTQTPS GF KYWIKER GTSLNDKAPF GCVIKTNPVR AENCAVGNIP VSMDIPDSAF TRVIDAPAVT NLECQVAVCT HSSDFGGIAT LTF KTDKPG KCAVHSHSNV ATIQEAAVDI KTDGKITLHF STASASPAFK VSVCSAKTTC MAACEPPKDH IVPYGASHNN QVFP DMSGT AMTWVQRVAG GFGGLTLAAV AVLILVTCVT MRR

UniProtKB: Structural polyprotein

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Macromolecule #2: E2 glycoprotein

MacromoleculeName: E2 glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Alphavirus M1
Molecular weightTheoretical: 46.462031 KDa
SequenceString: SVTKHFNVYK ATKPYLAYCA DCGDGQFCYS PVAIEKIRDE ASDGMIKIQV AAQIGINKGG THEHNKIRYI AGHDMKEANR DSLQVHTSG VCAIRGTMGH FIVAYCPPGG ELKVQFQDAE SHTQACKVQY KHAPAPVGRE KFTVRPHFGI EVPCTTYQLT T APTEEEID ...String:
SVTKHFNVYK ATKPYLAYCA DCGDGQFCYS PVAIEKIRDE ASDGMIKIQV AAQIGINKGG THEHNKIRYI AGHDMKEANR DSLQVHTSG VCAIRGTMGH FIVAYCPPGG ELKVQFQDAE SHTQACKVQY KHAPAPVGRE KFTVRPHFGI EVPCTTYQLT T APTEEEID MHTPPDIPDI TLLSQRSGNV KITAGGKTIR YNCTCGSGNV GTTSSDKTIN SCKIAQCHAA VTNHDKWQYT SS FVPRADQ LSRKGKVHVP FPLTNSTCRV PLARAPGVTY GKRELTVKLH PDHPTLLTYR SLGADPRPYE EWIDRYVERT IPV TEDGIE YRWGNNPPVR LWAQLTTEGK PHGWPHEIIL YYYGLYPAAT IVAVSAACLA VVLSLLASCY MFATARRKCL TPYA LTPGA VVPVTLGVLC CAPRAHA

UniProtKB: Structural polyprotein

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Macromolecule #3: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Alphavirus M1
Molecular weightTheoretical: 30.084988 KDa
SequenceString: MNYIPTQTFY GRRWRPRPAF RPWRVPMQPA PPMIPELQTP IVQAQQMQQL ISAVSALTTK QNGKAPKKPK KKPQKAKAKK NEQQKKNEN KKPPPKQKNP AKKKKPGKRE RMCMKIENDC IFEVKLDGKV TGYACLVGDK VMKPAHVKGV IDNPDLAKLT Y KKSSKYDL ...String:
MNYIPTQTFY GRRWRPRPAF RPWRVPMQPA PPMIPELQTP IVQAQQMQQL ISAVSALTTK QNGKAPKKPK KKPQKAKAKK NEQQKKNEN KKPPPKQKNP AKKKKPGKRE RMCMKIENDC IFEVKLDGKV TGYACLVGDK VMKPAHVKGV IDNPDLAKLT Y KKSSKYDL ECAQIPVHMK SDASKYTHEK PEGHYNWHHG AVQYSGGRFT IPTGAGKPGD SGRPIFDNKG RVVAIVLGGA NE GARTALS VVTWTKDMVT RYTPEGTEEW

UniProtKB: Structural polyprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr / Number images used: 32894
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: jspr
FSC plot (resolution estimation)

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