8EDJ: RA3G-ssRNA-GA

Crystal structure of rA3G-ssRNA-GA. Determined by X-ray diffraction at 1.83 Å resolution. Released 11 Jan 2023.

Method: X-ray diffraction
Resolution: 1.83 Å
Organisms: Macaca mulatta, synthetic construct
Chains: 2
Atoms: 3,566
Mol. weight: 48.45 kDa
Ligands: ZN
Released: 11 Jan 2023

Explore 8EDJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8EDJ contains 22 α-helices and 17 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: 22 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	5-8	4
α-helix	11	1
β-strand	12	1	1
α-helix	13	1
α-helix	14-21	8
β-strand	32-40	9	2
β-strand	50-57	8	2
α-helix	62-64	3
α-helix	66-79	14
β-strand	86-94	9	2
α-helix	98-109	12
β-strand	114-122	9	2
α-helix	129-140	12
β-strand	148-151	4	2
α-helix	154-164	11
β-strand	165	1	1
α-helix	170-172	3
α-helix	174-175	2
α-helix	178-192	15
β-strand	197	1	3
α-helix	199-206	8
α-helix	210-211	2
β-strand	219-228	10	4
β-strand	231-234	4	4
β-strand	240-243	4	4
β-strand	245	1	5
β-strand	256	1	5
α-helix	258-268	11
β-strand	276-284	9	4
α-helix	285-287	3
α-helix	288-300	13
β-strand	304-312	9	4
α-helix	320-329	10
β-strand	333-336	4	4
α-helix	339-349	11
β-strand	350	1	3
α-helix	355-357	3
α-helix	359-360	2
α-helix	363-379	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3G	A	protein	386	Macaca mulatta	Q7YR23 (AlphaFold model)
RNA (5'-r(pupgpapupupu)-3')	R	RNA	10	synthetic construct

Sequence of entity 1 (A), FASTA

>8EDJ_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A)
GPGGSGGMKPQIRNMVEPMDPRTFVSNFNNRPILSGLDTVWLCCEVKTKDPSGPPLDAKI
FQGKVYPKAKYHPEMRFLRWFHKWRQLHHDQEYKVTWYVSWSPCTRCANSVATFLAKDPK
VTLTIFVARLYYFWKPDYQQALRILAEAGATMKIMNYNEFQDCWNKFVDGRGKPFKPWNN
LPKHYTLLQATLGELLRHLMDPGTFTSNFNNKPWVSGQHETYLCYKVERLHNDTWVPLNQ
HRGFLRNQAPNIHGFPKGRHAALCFLDLIPFWKLDGQQYRVTCFTSWSPCFSCAQEMAKF
ISNNEHVSLCIFAARIYDDQGRYQEGLRTLHRDGAKIAMMNYSEFEYCWDTFVDRQGRPF
QPWDGLDEHSQALSGRLRAILQNQGN

Sequence of entity 2 (R), FASTA

>8EDJ_2 RNA (5'-R(P*UP*GP*AP*UP*UP*U)-3') (chains R)
UUUUGAUUUU

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural basis of sequence-specific RNA recognition by the antiviral factor APOBEC3G. Yang, H., Kim, K., Li, S. et al. Nat Commun (2022) 13:7498-7498. DOI 10.1038/s41467-022-35201-9 · PubMed

Other PDB entries of the same protein (UniProt Q7YR23 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8TX4 1.9 Å, Crystal Structure of rA3G-ssDNA-GA
8TVC 1.93 Å, Crystal structure of rA3G-ssDNA-AA
8E40 3.57 Å, Full-length APOBEC3G in complex with HIV-1 Vif, CBF-beta, and fork RNA

Browse structure collections

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