ISDA: 9E9V

Deposition Date 2024-11-08

Release Date 2026-03-11

Last Version Date 2026-03-11

Entry Detail

PDB ID:

9E9V

Keywords:

VIRAL PROTEIN/RNA

Title:

Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

Biological Source:

Source Organism(s):

Pan troglodytes (Taxon ID: 9598)
Homo sapiens (Taxon ID: 9606)
Human immunodeficiency virus 1 (Taxon ID: 11676)
Escherichia coli BL21(DE3) (Taxon ID: 469008)

Expression System(s):

Escherichia coli bl21(de3)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

4.00 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:single-stranded DNA cytosine deaminase
Gene (Uniprot):APOBEC3H
Chain IDs:A, B, E
Chain Length:183
Number of Molecules:3
Biological Source:Pan troglodytes

UniProt ID:B7T0U6 Pfam ID:PF18771

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*GP*CP*CP*GP*GP*G)-3')
Chain IDs:D (auth: C), G
Chain Length:9
Number of Molecules:2
Biological Source:Escherichia coli BL21(DE3)

Polymer Type:polyribonucleotide
Molecule:RNA (5'-R(P*CP*CP*CP*GP*GP*CP*A)-3')
Chain IDs:C (auth: D), F (auth: H)
Chain Length:10
Number of Molecules:2
Biological Source:Escherichia coli BL21(DE3)

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongin-B
Gene (Uniprot):ELOB
Chain IDs:I (auth: m)
Chain Length:102
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15370 Pfam ID:PF00240

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Elongin-C
Gene (Uniprot):ELOC
Chain IDs:H (auth: n)
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens

UniProt ID:Q15369 Pfam ID:PF03931

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Core-binding factor subunit beta
Gene (Uniprot):CBFB
Chain IDs:K (auth: o), M (auth: s)
Chain Length:170
Number of Molecules:2
Biological Source:Homo sapiens

UniProt ID:Q13951 Pfam ID:PF02312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Virion infectivity factor
Gene (Uniprot):vif
Chain IDs:J (auth: p), L (auth: t)
Chain Length:176
Number of Molecules:2
Biological Source:Human immunodeficiency virus 1

UniProt ID:P12504

Ligand Molecules

Primary Citation

HIV-1 vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to induce degradation.

Skorupka, K.A, Matsuoka, K, Hassan, B, Ghirlando, R, Balachandran, V, Chen, T.H, Walters, K.J, Schiffer, C.A, Wolf, M, Iwatani, Y, Matsuo, H.Show

Nat Commun 16 5879 5879 (2025)

PMID: 40593686 DOI: 10.1038/s41467-025-60984-y

Primary Citation of related structures

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