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- EMDB-34689: Pentamer of FMDV (A/TUR/14/98) -

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Basic information

Entry
Database: EMDB / ID: EMD-34689
TitlePentamer of FMDV (A/TUR/14/98)
Map data
Sample
  • Virus: Foot-and-mouth disease virus
    • Protein or peptide: VP1 of capsid protein
    • Protein or peptide: VP2 of capsid protein
    • Protein or peptide: VP3 of capsid protein
KeywordsVIRAL PROTEIN
Biological speciesFoot-and-mouth disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi HZ / Dong H
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural and in vivo studies of neutralizing antibody topographical classifications reveal mechanisms underlying differences in immunogenicity and antigenicity between 146S and 12S of foot- ...Title: Structural and in vivo studies of neutralizing antibody topographical classifications reveal mechanisms underlying differences in immunogenicity and antigenicity between 146S and 12S of foot-and-mouth disease virus
Authors: Li HZ / Dong H
History
DepositionNov 8, 2022-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34689.png

Downloads & links

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Map

FileDownload / File: emd_34689.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.49371 - 4.1549807
Average (Standard dev.)0.004116506 (±0.11097119)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 291.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34689_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34689_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Foot-and-mouth disease virus

EntireName: Foot-and-mouth disease virus
Components
  • Virus: Foot-and-mouth disease virus
    • Protein or peptide: VP1 of capsid protein
    • Protein or peptide: VP2 of capsid protein
    • Protein or peptide: VP3 of capsid protein

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Supramolecule #1: Foot-and-mouth disease virus

SupramoleculeName: Foot-and-mouth disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12110 / Sci species name: Foot-and-mouth disease virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP1 of capsid protein

MacromoleculeName: VP1 of capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.111094 KDa
SequenceString: TTSAGESADP VTTTVENYGG ETQVQRRHHT DVGFIMDRFV KINNTNPTHV IDLMQTHQHG LVGALLRAAT YYFSDLEIVV RHEGNLTWV PNGAPEAALS NAGNPTAYNK APFTRLALPY TAPHRVLATV YNGTSKYSTT GERTRGDLGA LAARVATQLP A SFNFGAIR ...String:
TTSAGESADP VTTTVENYGG ETQVQRRHHT DVGFIMDRFV KINNTNPTHV IDLMQTHQHG LVGALLRAAT YYFSDLEIVV RHEGNLTWV PNGAPEAALS NAGNPTAYNK APFTRLALPY TAPHRVLATV YNGTSKYSTT GERTRGDLGA LAARVATQLP A SFNFGAIR ATDISELLVR MKRAELYCPR PLLAVEVTAQ DRHKQKIIAP AKQ

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Macromolecule #2: VP2 of capsid protein

MacromoleculeName: VP2 of capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.575779 KDa
SequenceString: DKKTEETTLL EDRTLTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVTQAER FFKKHLFNWT TDKPFGHLEK LKLPTDHKG VYGHLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEW KKFTPREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY ...String:
DKKTEETTLL EDRTLTTRNG HTTSTTQSSV GVTYGYSTGE DHVSGPNTSG LETRVTQAER FFKKHLFNWT TDKPFGHLEK LKLPTDHKG VYGHLVDSFA YMRNGWDVEV SAVGNQFNGG CLLVAMVPEW KKFTPREKYQ LTLFPHQFIS PRTNMTAHIT V PYLGVNRY DQYKKHKPWT LVVMVVSPLT TSSIGATEIK VYANIAPTHV HVAGELPSKE

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Macromolecule #3: VP3 of capsid protein

MacromoleculeName: VP3 of capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 24.284121 KDa
SequenceString: GIVPVACSDG YGGLVTTDPK TADPVYGKVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTREDE QRLLAKFDVS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VETPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY ...String:
GIVPVACSDG YGGLVTTDPK TADPVYGKVY NPPRTNYPGR FTNLLDVAEA CPTFLCFDDG KPYVVTREDE QRLLAKFDVS LAAKHMSNT YLSGIAQYYA QYSGTINLHF MFTGSTDSKA RYMVAYVPPG VETPPDTPER AAHCIHAEWD TGLNSKFTFS I PYVSAADY AYTASDVAET TNVQGWVCIY QITHGKAQND TLVVSVSAGK DFELRLPIDP RTQ

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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: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 e/Å2

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192654

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