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- EMDB-38893: ASFV p72 in complex with Fab B1 -

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Basic information

Entry
Database: EMDB / ID: EMD-38893
TitleASFV p72 in complex with Fab B1
Map data
Sample
  • Complex: ASFV p72 in complex with Fab B1
    • Protein or peptide: Light chain of B1
    • Protein or peptide: Heavy chain of B1
  • 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: 2.75 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 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38893.png

Downloads & links

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Map

FileDownload / File: emd_38893.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.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.81
Minimum - Maximum-2.5639882 - 4.420989
Average (Standard dev.)0.0010685201 (±0.12826866)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : ASFV p72 in complex with Fab B1

EntireName: ASFV p72 in complex with Fab B1
Components
  • Complex: ASFV p72 in complex with Fab B1
    • Protein or peptide: Light chain of B1
    • Protein or peptide: Heavy chain of B1
  • Protein or peptide: B646L

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Supramolecule #1: ASFV p72 in complex with Fab B1

SupramoleculeName: ASFV p72 in complex with Fab B1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3
Source (natural)Organism: African swine fever virus

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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

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Macromolecule #2: Light chain of B1

MacromoleculeName: Light chain of B1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.302654 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
DIVLTQTPRS LSVSPGEPAS ISCRSSQSLE EYGKNWLSWY QQKPGQSPRL LIYQATNRAS WVPERFSGSG SGTDFTLKIS RVEAEDVGV YYCFQDLQPP NGFGAGTKLE LK

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Macromolecule #3: Heavy chain of B1

MacromoleculeName: Heavy chain of B1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 12.966524 KDa
Recombinant expressionOrganism: Sus scrofa (pig)
SequenceString:
EVKLVESGGG LVQPGGSLKL SCVGSGSTFS SDAVSWVRQA PGKGLEWLAG IDGDGGGGST YYADSVKGRF TISRDNSQKT AYLQMNSLR TDDTARYYCA ECPMVLLAKC SMEFWGPGVE VVVS

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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 KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 210044
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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