7UXD: DNA dC->dU-editing enzyme APOBEC-3G

Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine. Determined by X-ray diffraction at 1.5 Å resolution. Released 14 Dec 2022.

Method: X-ray diffraction
Resolution: 1.5 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 1,931
Mol. weight: 25.88 kDa
Ligands: ZN
Released: 14 Dec 2022

Explore 7UXD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7UXD contains 13 α-helices and 11 β-strands across 1 chain. 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: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	197	1	1
α-helix	199-206	8
β-strand	219-228	10	2
β-strand	231-243	13	2
α-helix	244	1
β-strand	245	1	3
α-helix	246	1
β-strand	249	1	4
β-strand	252	1	4
β-strand	256	1	3
α-helix	258-265	8
α-helix	266-269	4
β-strand	277-285	9	2
α-helix	286-288	3
α-helix	289-301	13
β-strand	305-313	9	2
α-helix	317-319	3
α-helix	321-330	10
β-strand	334-337	4	2
α-helix	340-350	11
β-strand	351	1	1
α-helix	356-358	3
α-helix	360-361	2
α-helix	364-379	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3G	A	protein	199	Homo sapiens	Q9HC16 (AlphaFold model)
DNA (5'-d(apaptpcpcp(ddn)papap*a)-3')	B	DNA	9	synthetic construct

Sequence of entity 1 (A), FASTA

>7UXD_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A)
GPLGSEILRHSMDPATFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLAQRRGFLANQ
AKHKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHV
SLCIKTARIYDDKGRAAEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWDGLD
EHSQDLSGRLRAILQNQEN

Sequence of entity 2 (B), FASTA

>7UXD_2 DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3') (chains B)
AATCCUAAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state. Maiti, A., Hedger, A.K., Myint, W. et al. Nat Commun (2022) 13:7117-7117. DOI 10.1038/s41467-022-34752-1 · PubMed

Other PDB entries of the same protein (UniProt Q9HC16 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3V4K 1.38 Å, First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase…
4ROW 1.7 Å, The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode…
4ROV 1.8 Å, The crystal structure of novel APOBEC3G CD2 head-to-tail dimer suggests the binding mode…
6BUX 1.86 Å, Crystal structure of APOBEC3G catalytic domain complex with substrate ssDNA
5ZVB 2.0 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dT9)
3V4J 2.04 Å, First-In-Class Small Molecule Inhibitors of the Single-strand DNA Cytosine Deaminase…
3IR2 2.25 Å, Crystal structure of the APOBEC3G catalytic domain
3E1U 2.3 Å, The Crystal Structure of the Anti-Viral APOBEC3G Catalytic Domain
3IQS 2.3 Å, Crystal structure of the anti-viral APOBEC3G catalytic domain
5ZVA 2.3 Å, APOBEC3F Chimeric Catalytic Domain in Complex with DNA(dC9)
8J62 2.5 Å, Cryo-EM structure of APOBEC3G-Vif complex
8CX0 2.7 Å, Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC monomeric complex

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