5W2M: DNA dC->dU-editing enzyme APOBEC-3F

APOBEC3F Catalytic Domain Complex with a Single-Stranded DNA. Determined by X-ray diffraction at 3.7 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,926
Mol. weight: 183.4 kDa
Ligands: ZN
Released: 13 Dec 2017

Explore 5W2M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5W2M contains 48 α-helices and 84 β-strands across 8 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.

Chains A, B, J and K: 6 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	192	1	1
β-strand	195	1	2
α-helix	197-203	7
β-strand	217-219	3	1
β-strand	220-225	6	3
β-strand	232-234	3	3
β-strand	237-239	3	1
α-helix	251-260	10
β-strand	268-273	6	3
β-strand	277	1	4
α-helix	281-293	13
β-strand	297-300	4	3
β-strand	301-303	3	5
β-strand	305	1	4
α-helix	312-320	9
β-strand	328-330	3	5
α-helix	333-342	10
β-strand	344	1	2
α-helix	357-371	15

Chains C, D and M: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	195	1	11
α-helix	197-204	8
β-strand	217-221	5	12
β-strand	224-225	2	12
β-strand	235-239	5	12
α-helix	251-260	10
β-strand	268-275	8	12
α-helix	283-288	6
β-strand	297-303	7	12
α-helix	312-321	10
β-strand	326-330	5	12
α-helix	333-343	11
β-strand	344	1	11
α-helix	357-371	15

Chain L: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	195	1	25
α-helix	197-204	8
β-strand	217-221	5	26
β-strand	224-225	2	26
β-strand	235-239	5	26
α-helix	251-260	10
β-strand	268-275	8	26
α-helix	283-288	6
β-strand	297-303	7	26
α-helix	312-323	12
β-strand	326-330	5	26
α-helix	333-343	11
β-strand	344	1	25
α-helix	357-371	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3F	A, B, C, D, J, K, L, M	protein	184	Homo sapiens	Q8IUX4 (AlphaFold model)
DNA (5'-d(ptptptptptptptptptpt)-3')	E, N	DNA	10	Homo sapiens

Sequence of entity 1 (A, B, C, D, J, K, L, M), FASTA

>5W2M_1 DNA dC->dU-editing enzyme APOBEC-3F (chains A, B, C, D, J, K, L, M)
NPMEAMYPHIFYFHFKNLRKAYGRNESWLCFTMEVVKHHSPVSWKRGVFRNQVDPETHCH
AERCFLSWFCDDILSPNTNYEVTWYTSWSPCPECAGEVAEFLARHSNVNLTIFTARLYYF
WDTDYQEGLRSLSQEGASVEIMGYKDFKYCWENFVYNDDEPFKPWKGLKYNFLFLDSKLQ
EILE

Sequence of entity 2 (E, N), FASTA

>5W2M_2 DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3') (chains E, N)
TTTTTTTTTT

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Molecular Interactions of a DNA Modifying Enzyme APOBEC3F Catalytic Domain with a Single-Stranded DNA. Fang, Y., Xiao, X., Li, S.X. et al. J Mol Biol (2018) 430:87-101. DOI 10.1016/j.jmb.2017.11.007 · 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
4J4J 3.1 Å, Crystal structure of the APOBEC3F Vif binding domain
6NIL 3.9 Å, cryoEM structure of the truncated HIV-1 Vif/CBFbeta/A3F complex

Browse structure collections

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