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- EMDB-60223: ASFV p72 in complex with Fab G6 -

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Basic information

Entry
Database: EMDB / ID: EMD-60223
TitleASFV p72 in complex with Fab G6
Map data
Sample
  • Complex: ASFV p72 in complex with Fab G6
    • Protein or peptide: G6 Light chain
    • Protein or peptide: G6 Heavy chain
    • Protein or peptide: B646L
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: 4.36 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
DepositionMay 17, 2024-
SupersessionOct 9, 2024ID: EMD-38897
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60223.png

Downloads & links

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Map

FileDownload / File: emd_60223.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.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.51
Minimum - Maximum-2.3708668 - 3.4405878
Average (Standard dev.)-0.0014922088 (±0.05870147)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60223_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_60223_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 : ASFV p72 in complex with Fab G6

EntireName: ASFV p72 in complex with Fab G6
Components
  • Complex: ASFV p72 in complex with Fab G6
    • Protein or peptide: G6 Light chain
    • Protein or peptide: G6 Heavy chain
    • Protein or peptide: B646L

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Supramolecule #1: ASFV p72 in complex with Fab G6

SupramoleculeName: ASFV p72 in complex with Fab G6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #3
Source (natural)Organism: African swine fever virus

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Macromolecule #1: G6 Heavy chain

MacromoleculeName: G6 Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 13.25496 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVKLVESGGG LVQPGGSLTL SCVGSGYTFS SYPICWVRQA PGKGLEWLSC IDSSGSKMHL ADSVLSRFTI SKDNSQNTAY LQMNSLRTE DTARYYCARG RWCYGVICDM DLWGPGVEVV VSS

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Macromolecule #2: G6 Light chain

MacromoleculeName: G6 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.384794 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IVLTQTPLSL SVSPGEPASI SCRSSQSLEE YGKNWLSWYQ QKPGQSPRLL IYQATNRASW VPERFSGSGS GTDFTLKISR VEAEDAGVY YCQQYKEFPW TFGQGTKLEL K

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Macromolecule #3: B646L

MacromoleculeName: B646L / type: protein_or_peptide / ID: 3 / 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

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265660
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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