[English] 日本語
Yorodumi
- EMDB-38894: ASFV p72 in complex with Fab C9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38894
TitleASFV p72 in complex with Fab C9
Map data
Sample
  • Complex: ASFV p72 in complex with Fab C9
    • Protein or peptide: B646L
    • Protein or peptide: Heavy chain of C9
    • Protein or peptide: Light chain of C9
KeywordsASFV / P72 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyMajor capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / B646L
Function and homology information
Biological speciesAfrican swine fever virus / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsWang X / Fu W / Yu Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Discov / Year: 2024
Title: p72 antigenic mapping reveals a potential supersite of vulnerability for African swine fever virus.
Authors: Qi Yu / Dening Liang / Wangjun Fu / Li Zhang / Jinglin Wang / Zhenjiang Zhang / Yao Sun / Dandan Zhu / BinYang Zheng / Ling Zhu / Ye Xiang / Dongming Zhao / Xiangxi Wang /
History
DepositionJan 29, 2024-
Header (metadata) releaseSep 4, 2024-
Map releaseSep 4, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38894.png

Downloads & links

-
Map

FileDownload / File: emd_38894.map.gz / Format: CCP4 / Size: 64 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 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å		1 Å/pix.
x 256 pix.
= 256. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0269
Minimum - Maximum-0.10870063 - 0.14341779
Average (Standard dev.)0.00019787642 (±0.0041792127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 256.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : ASFV p72 in complex with Fab C9

EntireName: ASFV p72 in complex with Fab C9
Components
  • Complex: ASFV p72 in complex with Fab C9
    • Protein or peptide: B646L
    • Protein or peptide: Heavy chain of C9
    • Protein or peptide: Light chain of C9

-
Supramolecule #1: ASFV p72 in complex with Fab C9

SupramoleculeName: ASFV p72 in complex with Fab C9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: African swine fever virus

-
Macromolecule #1: B646L

MacromoleculeName: B646L / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: African swine fever virus
Molecular weightTheoretical: 78.930531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHHHHHHHHH HGSDYKDHDG DYKDHDIDYK DDDDKELENL YFQGAGSMAS GGAFCLIAND GKADKIILAQ DLLNSRISNI KNVNKSYGK PDPEPTLSQI EETHLVHFNA HFKPYVPVGF EYNKVRPHTG TPTLGNKLTF GIPQYGDFFH DMVGHHILGA C HSSWQDAP ...String:
MHHHHHHHHH HGSDYKDHDG DYKDHDIDYK DDDDKELENL YFQGAGSMAS GGAFCLIAND GKADKIILAQ DLLNSRISNI KNVNKSYGK PDPEPTLSQI EETHLVHFNA HFKPYVPVGF EYNKVRPHTG TPTLGNKLTF GIPQYGDFFH DMVGHHILGA C HSSWQDAP IQGTSQMGAH GQLQTFPRNG YDWDNQTPLE GAVYTLVDPF GRPIVPGTKN AYRNLVYYCE YPGERLYENV RF DVNGNSL DEYSSDVTTL VRKFCIPGDK MTGYKHLVGQ EVSVEGTSGP LLCNIHDLHK PHQSKPILTD ENDTQRTCSH TNP KFLSQH FPENSHNIQT AGKQDITPIT DATYLDIRRN VHYSCNGPQT PKYYQPPLAL WIKLRFWFNE NVNLAIPSVS IPFG ERFIT IKLASQKDLV NEFPGLFVRQ SRFIAGRPSR RNIRFKPWFI PGVINEISLT NNELYINNLF VTPEIHNLFV KRVRF SLIR VHKTQVTHTN NNHHDEKLMS ALKWPIEYMF IGLKPTWNIS DQNPHQHRDW HKFGHVVNAI MQPTHHAEIS FQDRDT ALP DACSSISDIS PVTYPITLPI IKNISVTAHG INLIDKFPSK FCSSYIPFHY GGNAIKTPDD PGAMMITFAL KPREEYQ PS GHINVSRARE FYISWDTDYV GSITTADLVV SASAINFLLL QNGSAVLRYS T

UniProtKB: B646L

-
Macromolecule #2: Heavy chain of C9

MacromoleculeName: Heavy chain of C9 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.586333 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
EVKLVESGGG LVQPGGSLRL SCVGSGFTFS SYEINWVRQA PGKGLEWLAV VSKIGDRTYY ADSVRGRLTI SRDNSQNTAY LQMNSLRTE DTARYYCVRA WCASTCLPGD IMDLWGPGVG VVVSSL

-
Macromolecule #3: Light chain of C9

MacromoleculeName: Light chain of C9 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 11.621887 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
QTVIQEPAMS VSPGGTVTLT CAWSSGSVTT SNYPSWFQQT PGQPPRQLIY NTNSRPTGVP RRFSGKISGN KAALTITGAQ AEDEADYFC GLYKRSANNI FGGGTHLTVL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 223575
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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