6BWY: DNA substrate selection by APOBEC3G

DNA substrate selection by APOBEC3G. Determined by X-ray diffraction at 2.9 Å resolution. Released 18 Apr 2018.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: synthetic construct, Schizosaccharomyces pombe (strain 972 / ATCC 24843), Homo sapiens
Chains: 8
Atoms: 11,882
Mol. weight: 206.98 kDa
Ligands: ZN, PO4
Released: 18 Apr 2018

Explore 6BWY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BWY contains 45 α-helices and 61 β-strands across 4 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: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	1
β-strand	45-48	4	1
α-helix	50-53	4
β-strand	61-77	17	2
β-strand	85-92	8	2
β-strand	103-109	7	2
β-strand	124-134	11	2
β-strand	139-151	13	2
α-helix	164-167	4
β-strand	171	1	2
α-helix	177-190	14
α-helix	199-205	7
β-strand	219-228	10	3
β-strand	231-243	13	3
α-helix	258-264	7
β-strand	277-285	9	3
α-helix	289-301	13
β-strand	305-313	9	3
α-helix	321-330	10
β-strand	334-337	4	3
α-helix	340-349	10
α-helix	356-358	3
α-helix	360-361	2
α-helix	364-380	17

Chain B: 11 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	34-37	4
β-strand	39-42	4	4
β-strand	45-48	4	4
α-helix	50-53	4
β-strand	61-77	17	5
β-strand	85-92	8	5
β-strand	103-109	7	5
β-strand	124-134	11	5
β-strand	139-151	13	5
β-strand	171	1	5
α-helix	177-193	17
β-strand	197	1	6
α-helix	199-205	7
β-strand	219-228	10	7
β-strand	231-243	13	7
α-helix	258-265	8
α-helix	266-268	3
β-strand	277-285	9	7
α-helix	289-301	13
β-strand	305-313	9	7
α-helix	321-329	9
β-strand	334-337	4	7
α-helix	340-349	10
β-strand	351	1	6
α-helix	356-358	3
α-helix	365-378	14

Chain E: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	8
β-strand	45-48	4	8
α-helix	50-53	4
β-strand	61-77	17	9
β-strand	85-92	8	9
β-strand	103-109	7	9
β-strand	124-134	11	9
β-strand	139-151	13	9
β-strand	159	1	10
β-strand	171	1	9
α-helix	177-193	17
β-strand	197	1	11
α-helix	199-205	7
β-strand	219-228	10	12
β-strand	231-243	13	12
α-helix	258-265	8
α-helix	266-269	4
β-strand	277-285	9	12
α-helix	289-301	13
β-strand	305-313	9	12
α-helix	321-329	9
β-strand	334-337	4	12
α-helix	340-349	10
β-strand	351	1	11
α-helix	356-358	3
α-helix	360-361	2
α-helix	364-378	15

Chain G: 12 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	39-42	4	13
β-strand	45-48	4	13
α-helix	50-53	4
β-strand	61-77	17	14
β-strand	85-92	8	14
β-strand	103-109	7	14
β-strand	124-134	11	14
β-strand	139-151	13	14
β-strand	159	1	10
β-strand	171	1	14
α-helix	177-190	14
β-strand	197	1	15
α-helix	199-205	7
β-strand	219-228	10	16
β-strand	231-234	4	16
α-helix	236-238	3
β-strand	240-243	4	16
α-helix	258-264	7
α-helix	267-269	3
β-strand	277-285	9	16
α-helix	289-301	13
β-strand	305-313	9	16
α-helix	321-329	9
β-strand	334-337	4	16
α-helix	340-349	10
β-strand	351	1	15
α-helix	356-358	3
α-helix	360-361	2
α-helix	364-378	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (30-mer)	C, D, F, I	DNA	30	synthetic construct
Protection of telomeres protein 1, DNA dC->dU-editing enzyme APOBEC-3G fusion	A, B, E, G	protein	361	Schizosaccharomyces pombe (strain 972 / ATCC 24843), Homo sapiens	O13988 (AlphaFold model), Q9HC16 (AlphaFold model)

Sequence of entity 1 (C, D, F, I), FASTA

>6BWY_1 DNA (30-MER) (chains C, D, F, I)
AGAAGACCCAAAGAAGAGGAAGCAGGTTAC

Sequence of entity 2 (A, B, E, G), FASTA

>6BWY_2 Protection of telomeres protein 1, DNA dC-&gt;dU-editing enzyme APOBEC-3G fusion (chains A, B, E, G)
MVIDSLQLNELLNAGEYKIGELTFQSIRSSQELQKKNTIVNLFGIVKDFTPSRQSLHGTK
DWVTTVYLWDPTCDTSSIGLQIHLFSKQGNDLPVIKQVGQPLLLHQITLRSYRDRTQGLS
KDQFRYALWPDFSSNSKDTLCPQPMPRLMKTGDKEEQFALLLNKIWDEQTNHSMDPPTFT
FNFNNEPWVRGRHETYLCYEVERMHNDTWVKLNQRRGFLANQAPHKHGFLEGRHAELCFL
DVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHVSLCIKTARIYDDQGRAQE
GLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWDGLDEHSQDLSGRLRAILQNQE
N

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
PO4	Phosphate ion	O4 P	15

Primary citation

Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies. Ziegler, S.J., Liu, C., Landau, M. et al. PLoS One (2018) 13:e0195048-e0195048. DOI 10.1371/journal.pone.0195048 · PubMed

Other PDB entries of the same protein (UniProt O13988 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5USB 1.61 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera…
4HIK 1.64 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTACGGT)
4HIM 1.75 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGATACGGT)
4HIO 1.75 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTAACGGT)
4HJ7 1.78 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTAGGGT)
4HID 1.82 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GCTTACGGT)
4HJ9 1.85 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (CGGTTACGGT)
1QZG 1.9 Å, Crystal structure of Pot1 (protection of telomere)- ssDNA complex
5USN 1.9 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera…
5USO 2.0 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssRNA/ssDNA chimera…
4HJ5 2.04 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTTCGGT)
4HJ8 2.04 Å, Crystal Structure of Schizosaccharomyces pombe Pot1pC bound to ssDNA (GGTTACGCT)

Browse structure collections

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