5ZVB: APOBEC3F Chimeric Catalytic Domain

APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9). Determined by X-ray diffraction at 2.0 Å resolution. Released 21 Nov 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Homo sapiens, DNA-binding vector pODB80
Chains: 3
Atoms: 3,478
Mol. weight: 53.42 kDa
Ligands: CAC, ZN
Released: 21 Nov 2018

Explore 5ZVB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5ZVB contains 24 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: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	-28--27	2	1
α-helix	-24	1
β-strand	-23	1	2
α-helix	-22	1
α-helix	-21--14	8
β-strand	-1-226	10	1
β-strand	232-239	8	1
α-helix	250-257	8
α-helix	258-262	5
β-strand	267-277	11	1
α-helix	278-280	3
α-helix	281-293	13
β-strand	297-305	9	1
α-helix	312-323	12
β-strand	327-330	4	1
α-helix	333-342	10
β-strand	344	1	2
α-helix	349-351	3
α-helix	353-354	2
α-helix	357-372	16

Chain B: 12 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	-28--27	2	3
α-helix	-24	1
β-strand	-23	1	4
α-helix	-22	1
α-helix	-21--14	8
β-strand	-1-225	9	3
β-strand	232-239	8	3
β-strand	241	1	5
β-strand	248	1	5
α-helix	250-257	8
α-helix	258-262	5
β-strand	268-277	10	3
α-helix	278-280	3
α-helix	281-293	13
β-strand	297-305	9	3
α-helix	312-323	12
β-strand	327-330	4	3
α-helix	333-342	10
β-strand	344	1	4
α-helix	349-351	3
α-helix	353-354	2
α-helix	357-372	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
APEBEC3F/ssDNA-T9	A, B	protein	209	Homo sapiens	Q8IUX4 (AlphaFold model), Q9HC16 (AlphaFold model)
DNA (5'-d(aptptptptpcpapap*t)-3')	C	DNA	9	DNA-binding vector pODB80

Sequence of entity 1 (A, B), FASTA

>5ZVB_1 APEBEC3F/ssDNA-T9 (chains A, B)
MAHHHHHHVDDDDKMLVPRGSENLYFQGSAMDPPTFTFNFNNEPWVRGRHETYLCFTMEV
VKHHSPVSWKRGVFRNQVDPETHCHAERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECA
GEVAEFLARHSNVNLTIFTARLYYFWDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFV
YNDDEPFKPWKGLKYNFLFLDSKLQEILE

Sequence of entity 2 (C), FASTA

>5ZVB_2 DNA (5'-D(*AP*TP*TP*TP*TP*CP*AP*AP*T)-3') (chains C)
ATTTTCAAT

Ligands and cofactors

ID	Name	Formula	Copies
CAC	Cacodylate ion	C2 H6 As O2	2
ZN	Zinc ion	Zn	2

Primary citation

Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA. Cheng, C., Zhang, T., Wang, C. et al. Chin J Chem (2018) 36:1241-1248. DOI 10.1002/cjoc.201800508

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
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
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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