8CX2: DNA dC->dU-editing enzyme APOBEC-3G

Cryo-EM structure of human APOBEC3G/HIV-1 Vif/CBFbeta/ELOB/ELOC dimeric complex in State 2. Determined by electron microscopy at 3.2 Å resolution. Released 15 Feb 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, Spodoptera frugiperda
Chains: 12
Atoms: 15,041
Mol. weight: 245.62 kDa
Ligands: ZN
Released: 15 Feb 2023

Explore 8CX2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CX2 contains 89 α-helices and 84 β-strands across 10 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: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	1
β-strand	12	1	2
α-helix	14-20	7
β-strand	32	1	3
β-strand	35-41	7	1
β-strand	50-54	5	1
β-strand	57	1	3
α-helix	62-64	3
α-helix	66-77	12
β-strand	86-94	9	1
α-helix	98-110	13
β-strand	114-122	9	1
α-helix	129-135	7
α-helix	136-140	5
α-helix	145-146	2
β-strand	147-151	5	1
α-helix	154-163	10
β-strand	165	1	2
α-helix	178-193	16
β-strand	197	1	4
α-helix	199-205	7
β-strand	219-228	10	5
β-strand	231-243	13	5
α-helix	244-247	4
α-helix	255-257	3
α-helix	258-265	8
α-helix	266-269	4
β-strand	277-283	7	5
α-helix	289-301	13
β-strand	305-311	7	5
α-helix	320-331	12
β-strand	334-337	4	5
α-helix	340-350	11
β-strand	351	1	4
α-helix	364-380	17

Chain B: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	6
β-strand	11-13	3	6
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	6
α-helix	43-45	3
β-strand	51-59	9	6
β-strand	62-69	8	6
β-strand	83-91	9	6
β-strand	94-97	4	6
α-helix	100-108	9
β-strand	116	1	7
α-helix	119-125	7
α-helix	137-139	3
α-helix	145-153	9
α-helix	155-157	3
α-helix	162-164	3
α-helix	166-169	4

Chain C: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-15	8
β-strand	25-29	5	6
α-helix	37-50	14
β-strand	55-59	5	6
β-strand	65-70	6	6
α-helix	71-74	4
β-strand	85-87	3	6
β-strand	94-103	10	6
β-strand	106-115	10	6
β-strand	120-127	8	6
α-helix	130-134	5
α-helix	137-148	12
β-strand	155	1	7

Chain D: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	8
β-strand	12-18	7	8
β-strand	23	1	9
α-helix	24-35	12
β-strand	43-45	3	8
β-strand	50	1	8
α-helix	51-52	2
β-strand	56	1	9
α-helix	57-60	4
β-strand	68	1	10
β-strand	71	1	10
α-helix	72	1
β-strand	73-78	6	8
α-helix	91-93	3

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	8
β-strand	27-32	6	8
α-helix	33-37	5
α-helix	40-45	6
β-strand	59-61	3	8
α-helix	67-83	17
α-helix	90-92	3
α-helix	97-110	14

Chain F: 20 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	11
α-helix	14-21	8
β-strand	32-41	10	11
β-strand	50-57	8	11
α-helix	62-64	3
α-helix	66-77	12
β-strand	86-92	7	11
α-helix	98-110	13
β-strand	114-120	7	11
α-helix	129-135	7
α-helix	136-140	5
β-strand	147-151	5	11
α-helix	154-164	11
α-helix	178-193	16
β-strand	197	1	12
α-helix	199-206	8
β-strand	219-228	10	13
β-strand	231-243	13	13
α-helix	244	1
β-strand	245	1	14
α-helix	246-247	2
α-helix	255	1
β-strand	256	1	14
α-helix	257	1
α-helix	258-265	8
α-helix	266-269	4
β-strand	277-285	9	13
α-helix	289-301	13
β-strand	305-313	9	13
α-helix	321-331	11
β-strand	334-337	4	13
α-helix	340-350	11
β-strand	351	1	12
α-helix	356-358	3
α-helix	364-380	17

Chain G: 12 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	5-9	5	15
β-strand	11-13	3	15
α-helix	15-30	16
α-helix	33-35	3
β-strand	39-41	3	15
β-strand	51-59	9	15
β-strand	62-69	8	15
β-strand	83-91	9	15
β-strand	94-97	4	15
α-helix	100-108	9
α-helix	119-125	7
α-helix	127-129	3
α-helix	132-133	2
α-helix	136-139	4
α-helix	145-153	9
α-helix	155-157	3
α-helix	162-164	3
α-helix	166-169	4

Chain H: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	5-14	10
β-strand	25-29	5	15
α-helix	37-50	14
β-strand	55-59	5	15
β-strand	65-70	6	15
β-strand	85-87	3	15
β-strand	94-103	10	15
β-strand	106-115	10	15
β-strand	120-127	8	15
α-helix	130-134	5
α-helix	137-146	10

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA dC->dU-editing enzyme APOBEC-3G	A, F	protein	421	Homo sapiens	Q9HC16 (AlphaFold model)
Virion infectivity factor	B, G	protein	192	Human immunodeficiency virus 1	P69723
Core-binding factor subunit beta	C, H	protein	182	Homo sapiens	Q13951 (AlphaFold model)
Elongin-B	D, I	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	E, J	protein	112	Homo sapiens	Q15369
RNA (5'-r(papapupapapapapap*u)-3')	K	RNA	9	Spodoptera frugiperda
RNA (5'-r(pupupupapapapapap*u)-3')	L	RNA	9	Spodoptera frugiperda

Sequence of entity 1 (A, F), FASTA

>8CX2_1 DNA dC->dU-editing enzyme APOBEC-3G (chains A, F)
MKPHFRNTVERMYRDTFSYNFYNRPILSRRNTVWLCYEVKTKGPSRPPLDAKIFRGQVYS
ELKYHPEMRFFHWFSKWRKLHRDQEYEVTWYISWSPCTKCTRDMATFLAEDPKVTLTIFV
ARLYYFWDPDYQEALRSLCQKRDGPRATMKIMNYDEFQHCWSKFVYSQRELFEPWNNLPK
YYILLHIMLGEILRHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVLLNQRRG
FLCNQAPHKHGFLEGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFIS
KNKHVSLCIFTARIYDDQGRCQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGCPFQP
WDGLDEHSQDLSGRLRAILQNQENGSSLEGGGGWSHPQFEKGGGSGGGSGGGSWSHPQFE
K

Sequence of entity 2 (B, G), FASTA

>8CX2_2 Virion infectivity factor (chains B, G)
MENRWQVMIVWQVDRMRIRTWKSLVKHHMYVSGKARGWFYRHHYESPHPRISSEVHIPLG
DARLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPELADQLIHLYYFDCFSDSAI
RKALLGHIVSPRCEYQAGHNKVGSLQYLALAALITPKKIKPPLPSVTKLTEDRWNKPQKT
KGHRGSHTMNGH

Sequence of entity 3 (C, H), FASTA

>8CX2_3 Core-binding factor subunit beta (chains C, H)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQLLAVTGKKTT
RP

Sequence of entity 4 (D, I), FASTA

>8CX2_4 Elongin-B (chains D, I)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 5 (E, J), FASTA

>8CX2_5 Elongin-C (chains E, J)
MDGEEKTYGGCEGPDAMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEV
NFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 6 (K), FASTA

>8CX2_6 RNA (5'-R(P*AP*AP*UP*AP*AP*AP*AP*AP*U)-3') (chains K)
AAUAAAAAU

Sequence of entity 7 (L), FASTA

>8CX2_7 RNA (5'-R(P*UP*UP*UP*AP*AP*AP*AP*AP*U)-3') (chains L)
UUUAAAAAU

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

The structural basis for HIV-1 Vif antagonism of human APOBEC3G. Li, Y.L., Langley, C.A., Azumaya, C.M. et al. Nature (2023) 615:728-733. DOI 10.1038/s41586-023-05779-1 · 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…
7UXD 1.5 Å, Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy…
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

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