4J4J: APOBEC3F Vif binding domain

Crystal structure of the APOBEC3F Vif binding domain. Determined by X-ray diffraction at 3.1 Å resolution. Released 6 Nov 2013.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,006
Mol. weight: 49.97 kDa
Ligands: ZN
Released: 6 Nov 2013

Explore 4J4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4J4J contains 21 α-helices and 17 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, 7 β-strands

Element	Residues	Length	Sheet
α-helix	-24	1
β-strand	-23	1	1
α-helix	-22	1
α-helix	-21--14	8
β-strand	-3-226	12	2
β-strand	229-241	13	2
α-helix	250-261	12
β-strand	268-275	8	2
α-helix	281-292	12
β-strand	297-303	7	2
α-helix	312-323	12
β-strand	326-330	5	2
α-helix	333-342	10
β-strand	344	1	1
α-helix	349-351	3
α-helix	353-354	2
α-helix	357-372	16

Chain B: 11 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	-24	1
β-strand	-23	1	3
α-helix	-22	1
α-helix	-21--14	8
β-strand	-3-224	10	4
β-strand	226	1	5
β-strand	229	1	5
β-strand	233-241	9	4
β-strand	249	1	4
α-helix	250-261	12
β-strand	269-277	9	4
α-helix	278-280	3
α-helix	281-292	12
β-strand	297-305	9	4
α-helix	312-322	11
β-strand	326-329	4	4
α-helix	333-342	10
β-strand	344	1	3
α-helix	349-351	3
α-helix	353-354	2
α-helix	357-372	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3F	A, B	protein	209	Homo sapiens	Q8IUX4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4J4J_1 DNA dC->dU-editing enzyme APOBEC-3F (chains A, B)
MAHHHHHHVDDDDKMLVPRGSENLYFQGSAMDPPTFTFNFNNEPWVRGRHETYLCFTMEV
VKHHSPVSWKRGVFRNQVDPETHCHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECA
GEVAEFLARHSNVNLTIFTARLYYFWDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFV
YNDDEPFKPWKGLKYNFLFLDSKLQEILE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural determinants of HIV-1 Vif susceptibility and DNA binding in APOBEC3F. Siu, K.K., Sultana, A., Azimi, F.C. et al. Nat Commun (2013) 4:2593-2593. DOI 10.1038/ncomms3593 · 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
8VUD 2.6 Å, Crystal structure of APOBEC3F-CD1
4IOU 2.75 Å, Crystal structure of the HIV-1 Vif binding, catalytically active domain of APOBEC3F
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

About this viewer

MolViewer shows 4J4J directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.