[English] 日本語
Yorodumi
- EMDB-30845: FMDV capsid in complex with M170 Nab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30845
TitleFMDV capsid in complex with M170 Nab
Map data
Sample
  • Complex: FMDV in complex with M170Foot-and-mouth disease virus
    • Complex: FMDVFoot-and-mouth disease virus
      • 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
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-
UpdateMay 25, 2022-
Current statusMay 25, 2022Processing site: PDBj / Status: Released

-
Structure visualization

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

emd_30845.png

Downloads & links

-
Map

FileDownload / File: emd_30845.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
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

-
Supplemental data

-
Sample components

-
Entire : FMDV in complex with M170

EntireName: FMDV in complex with M170Foot-and-mouth disease virus
Components
  • Complex: FMDV in complex with M170Foot-and-mouth disease virus
    • Complex: FMDVFoot-and-mouth disease virus
      • 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

-
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

-
Supramolecule #2: FMDV

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

-
Supramolecule #3: M170

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

-
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

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more