8VUD: APOBEC3F-CD1

Crystal structure of APOBEC3F-CD1. Determined by X-ray diffraction at 2.6 Å resolution. Released 30 Jul 2025.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,139
Mol. weight: 46.76 kDa
Ligands: ZN
Released: 30 Jul 2025

Explore 8VUD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VUD contains 19 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11	1
β-strand	12	1	1
α-helix	13	1
α-helix	14-20	7
β-strand	34-40	7	2
α-helix	45-46	2
β-strand	52-59	8	2
β-strand	61	1	3
β-strand	64	1	3
α-helix	66-77	12
β-strand	85-93	9	2
α-helix	97-109	13
β-strand	113-121	9	2
α-helix	128-139	12
β-strand	142-146	5	2
α-helix	149-159	11
β-strand	160	1	1
α-helix	165-167	3
α-helix	173-188	16

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	11	1
β-strand	12	1	4
α-helix	13	1
α-helix	14-20	7
β-strand	34-40	7	5
β-strand	54-59	6	5
β-strand	61	1	6
β-strand	64	1	6
α-helix	66-77	12
β-strand	85-93	9	5
α-helix	97-109	13
β-strand	113-121	9	5
α-helix	128-139	12
β-strand	142-146	5	5
α-helix	149-159	11
β-strand	160	1	4
α-helix	165-167	3
α-helix	173-188	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3F	A, B	protein	197	Homo sapiens	Q8IUX4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8VUD_1 DNA dC->dU-editing enzyme APOBEC-3F (chains A, B)
GPGGSGGMKPHFRNTVERMDRDTFSYNFYNEPILARRNTVWLCYEVKTKGPSRPRLDAKI
FRGQVYSQPEHHAEMCFLSWFCGNQLPADKCFQITWFVSWTPCPDCVAKLAEFLAEHPNV
TLTISAARLYYYSERDYRRALCRLSQAGARVKIMDDEEFAYCWENFVDSEGQPFMPWYKF
DDNYAFLHRTLKEILRN

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Both Domains of APOBEC3F Recognize AA RNA Motifs to Support HIV-1 Virion Encapsidation and Antiviral Function. Pacheco, J., Yousefi, M., Yang, H. et al. J Mol Biol (2025) 438:169536-169536. DOI 10.1016/j.jmb.2025.169536 · PubMed

Other PDB entries of the same protein (UniProt Q8IUX4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5HX4 1.92 Å, Zinc-Free APOBEC3F Catalytic Domain Crystal Structure
5ZVB 2.0 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)
5ZVA 2.3 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9)
5HX5 2.33 Å, APOBEC3F Catalytic Domain Crystal Structure
3WUS 2.54 Å, Crystal Structure of the Vif-Binding Domain of Human APOBEC3F
4IOU 2.75 Å, Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F
4J4J 3.1 Å, Crystal structure of the APOBEC3F Vif binding domain
5W2M 3.7 Å, APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA
6NIL 3.9 Å, cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex

Browse structure collections

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