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- EMDB-34630: FMDV (A/TUR/14/98) in complex with M678F -

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Basic information

Entry
Database: EMDB / ID: EMD-34630
TitleFMDV (A/TUR/14/98) in complex with M678F
Map data
Sample
  • Complex: FMDV capsid protein in complex with M678F nab
    • Protein or peptide: VP1 of capsid protein
    • Protein or peptide: VP2 of capsid protein
    • Protein or peptide: VP3 of capsid protein
    • Protein or peptide: VP4 of capsid protein
    • Protein or peptide: M678F nab
KeywordsFMDV / antibody / VIRUS
Function / homology
Function and homology information


icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / cytoplasm
Similarity search - Function
Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus A / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLi HZ / Dong H / Liu P
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 / Liu P
History
DepositionOct 28, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34630.png

Downloads & links

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Map

FileDownload / File: emd_34630.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09142474 - 0.14776476
Average (Standard dev.)0.0013871321 (±0.0087655345)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 475.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34630_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_34630_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 : FMDV capsid protein in complex with M678F nab

EntireName: FMDV capsid protein in complex with M678F nab
Components
  • Complex: FMDV capsid protein in complex with M678F nab
    • Protein or peptide: VP1 of capsid protein
    • Protein or peptide: VP2 of capsid protein
    • Protein or peptide: VP3 of capsid protein
    • Protein or peptide: VP4 of capsid protein
    • Protein or peptide: M678F nab

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Supramolecule #1: FMDV capsid protein in complex with M678F nab

SupramoleculeName: FMDV capsid protein in complex with M678F nab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Foot-and-mouth disease virus A

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Macromolecule #1: VP1 of capsid protein

MacromoleculeName: VP1 of capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
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

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2 of capsid protein

MacromoleculeName: VP2 of capsid protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
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

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3 of capsid protein

MacromoleculeName: VP3 of capsid protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
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

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4 of capsid protein

MacromoleculeName: VP4 of capsid protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus A
Molecular weightTheoretical: 8.778129 KDa
SequenceString:
GAGQSSPATG SQNQSGNTGS IINNYYMQQY QNSMDTQLGD NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA

UniProtKB: Genome polyprotein

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Macromolecule #5: M678F nab

MacromoleculeName: M678F nab / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.753181 KDa
Recombinant expressionOrganism: Yeast centromeric expression vector p416TEF (others)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCVYSGGAYS MGWYRQAPGK QRELVAAITD DGITNYRDTV KGRFTISRDN AKKAVYLQMN SLKPEDTAV YHCNTVRRVA TLSGSSSGSW GQGTQVTVSS

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46708

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