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- EMDB-30845: FMDV capsid in complex with M170 Nab -

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Basic information

Entry
Database: EMDB / ID: EMD-30845
TitleFMDV capsid in complex with M170 Nab
Map data
Sample
  • Complex: FMDV in complex with M170
    • Complex: FMDV
      • Protein or peptide: VP1 of O type FMDV capsid
      • Protein or peptide: VP2 of O type FMDV capsid
      • Protein or peptide: VP3 of O type FMDV capsid
      • Protein or peptide: VP4 of O type FMDV capsid
    • Complex: M170
      • Protein or peptide: M170 Nab
KeywordsFMDV capsid in complex with M170 Nab / VIRUS
Biological speciesFoot-and-mouth disease virus / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsDong H / Liu P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)No. 31941011, 12034006, 31672592, 31873023, 31811540395, 31772739, 315725153 and 1811540395 China
CitationJournal: Protein Cell / Year: 2022
Title: Structural and molecular basis for foot-and-mouth disease virus neutralization by two potent protective antibodies.
Authors: Hu Dong / Pan Liu / Manyuan Bai / Kang Wang / Rui Feng / Dandan Zhu / Yao Sun / Suyu Mu / Haozhou Li / Michiel Harmsen / Shiqi Sun / Xiangxi Wang / Huichen Guo /
History
DepositionJan 2, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7dst
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7dst
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30845.png

Downloads & links

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Map

FileDownload / File: emd_30845.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å		1.35 Å/pix.
x 360 pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07847183 - 0.15951948
Average (Standard dev.)0.0007948838 (±0.010495215)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0780.1600.001

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Supplemental data

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Sample components

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Entire : FMDV in complex with M170

EntireName: FMDV in complex with M170
Components
  • Complex: FMDV in complex with M170
    • Complex: FMDV
      • Protein or peptide: VP1 of O type FMDV capsid
      • Protein or peptide: VP2 of O type FMDV capsid
      • Protein or peptide: VP3 of O type FMDV capsid
      • Protein or peptide: VP4 of O type FMDV capsid
    • Complex: M170
      • Protein or peptide: M170 Nab

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Supramolecule #1: FMDV in complex with M170

SupramoleculeName: FMDV in complex with M170 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Foot-and-mouth disease virus

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Supramolecule #2: FMDV

SupramoleculeName: FMDV / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Lama glama (llama)

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Supramolecule #3: M170

SupramoleculeName: M170 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5

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Macromolecule #1: VP1 of O type FMDV capsid

MacromoleculeName: VP1 of O type FMDV capsid / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 22.849139 KDa
SequenceString: TTSTGESADP VTATVENYGG ETQVQRRHHT DVSFILDRFV KVTPKDSINV LDLMQTPSHT LVGALLRTAT YYFADLEVAV KHKGDLTWV PNGAPVAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGKCKYAEG SLPNVRGDLQ VLAQKAARPL P TSFNYGAI ...String:
TTSTGESADP VTATVENYGG ETQVQRRHHT DVSFILDRFV KVTPKDSINV LDLMQTPSHT LVGALLRTAT YYFADLEVAV KHKGDLTWV PNGAPVAALD NTTNPTAYHK APLTRLALPY TAPHRVLATV YNGKCKYAEG SLPNVRGDLQ VLAQKAARPL P TSFNYGAI KATRVTELLY RMKRAETYCP RPLLAVHPSA ARHKQKIVAP

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Macromolecule #2: VP2 of O type FMDV capsid

MacromoleculeName: VP2 of O type FMDV capsid / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.091078 KDa
SequenceString: RILTTRNGHT TSTTQSSVGI THGYATAEDF VNGPNTSGLE TRVVQAERFF KTHLFDWVTS DPFGRYYLLE LPTDHKGVYG SLTDSYAYM RNGWDVEVTA VGNQFNGGCL LVAMVPELCS IEQRELFQLT LFPHQFINPR TNMTAHIKVP FVGVNRYDQY K VHKPWTLV ...String:
RILTTRNGHT TSTTQSSVGI THGYATAEDF VNGPNTSGLE TRVVQAERFF KTHLFDWVTS DPFGRYYLLE LPTDHKGVYG SLTDSYAYM RNGWDVEVTA VGNQFNGGCL LVAMVPELCS IEQRELFQLT LFPHQFINPR TNMTAHIKVP FVGVNRYDQY K VHKPWTLV VMVVAPLTVN TEGAPQIKVY ANIAPTNVHV AGEFPSKE

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Macromolecule #3: VP3 of O type FMDV capsid

MacromoleculeName: VP3 of O type FMDV capsid / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 23.754705 KDa
SequenceString: GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNMLPGR FTNLLDVAEA CPTFLHFDGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTVNLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA ...String:
GIFPVACSDG YGGLVTTDPK TADPVYGKVF NPPRNMLPGR FTNLLDVAEA CPTFLHFDGD VPYVTTKTDS DRVLAQFDLS LAAKHMSNT FLAGLAQYYT QYSGTVNLHF MFTGPTDAKA RYMIAYAPPG MEPPKTPEAA AHCIHAEWDT GLNSKFTFSI P YLSAADYA YTASDAAETT NVQGWVCLFQ ITHGKAEGDA LVVLASAGKD FELRLPVDAR Q

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Macromolecule #4: VP4 of O type FMDV capsid

MacromoleculeName: VP4 of O type FMDV capsid / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Foot-and-mouth disease virus
Molecular weightTheoretical: 7.963328 KDa
SequenceString:
SQNQSGNTGS IINNYYMQQY QNSMDTQLGN NAISGGSNEG STDTTSTHTT NTQNNDWFSK LASSAFSGLF GALLA

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Macromolecule #5: M170 Nab

MacromoleculeName: M170 Nab / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 12.939211 KDa
Recombinant expressionOrganism: Lama glama (llama)
SequenceString:
GGSQVQLQES GGGLVQAGGS LRLSCAASGR TFSSYAMGWF RQAPGSEREF VARISWSGGS TYYADSVKGR FTISRDNAKN TVYLQMNSL KPEDTAVYYC TAGFALPPSD YWGQGTQVTV SS

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3692
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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