5HX5: APOBEC3F Catalytic Domain Crystal Structure

APOBEC3F Catalytic Domain Crystal Structure. Determined by X-ray diffraction at 2.33 Å resolution. Released 18 May 2016.

Method: X-ray diffraction
Resolution: 2.33 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,944
Mol. weight: 46.85 kDa
Ligands: ZN
Released: 18 May 2016

Explore 5HX5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HX5 contains 19 α-helices and 16 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	192	1	1
β-strand	195	1	2
α-helix	197-204	8
α-helix	209-212	4
β-strand	217-225	9	1
β-strand	232-239	8	1
α-helix	250-261	12
β-strand	268-277	10	1
α-helix	278-280	3
α-helix	281-292	12
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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	192	1	3
β-strand	195	1	4
α-helix	197-204	8
β-strand	217-226	10	3
β-strand	232-239	8	3
α-helix	250-261	12
β-strand	267-275	9	3
α-helix	278-280	3
α-helix	281-292	12
β-strand	297-303	7	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
DNA dC->dU-editing enzyme APOBEC-3F	A, B	protein	199	Homo sapiens	Q8IUX4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5HX5_1 DNA dC->dU-editing enzyme APOBEC-3F (chains A, B)
GPLGSPGIPGKEILRNPMEAMDPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWK
RGVFRNQVDPETGRHAERCFLSWFADDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARH
SNVNLTIKTARLYYFDDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPW
DGLDYNFLDLDSKLQEILE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

1.92 Angstrom Zinc-Free APOBEC3F Catalytic Domain Crystal Structure. Shaban, N.M., Shi, K., Li, M. et al. J Mol Biol (2016) 428:2307-2316. DOI 10.1016/j.jmb.2016.04.026 · 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)
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

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