8H0I: APOBEC3G-Vif complex

Cryo-EM structure of APOBEC3G-Vif complex. Determined by electron microscopy at 2.8 Å resolution. Released 19 Jul 2023.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1, synthetic construct
Chains: 12
Atoms: 15,018
Mol. weight: 248.32 kDa
Ligands: ZN
Released: 19 Jul 2023

Explore 8H0I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H0I contains 70 α-helices and 81 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.

Chains A and B: 17 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	1	1	1
α-helix	3-9	7
β-strand	23-32	10	2
β-strand	35-47	13	2
α-helix	54-65	12
β-strand	73-81	9	2
α-helix	85-97	13
β-strand	101-109	9	2
α-helix	116-127	12
β-strand	131-134	4	2
α-helix	137-147	11
β-strand	148	1	1
α-helix	153-155	3
α-helix	157-158	2
α-helix	161-176	16
β-strand	180	1	3
α-helix	182-188	7
β-strand	203-210	8	4
β-strand	215-225	11	4
α-helix	241-248	8
α-helix	249-252	4
β-strand	260-266	7	4
α-helix	269-270	2
α-helix	272-284	13
β-strand	288-294	7	4
α-helix	306-314	9
β-strand	317-320	4	4
α-helix	323-333	11
β-strand	334	1	3
α-helix	343-344	2
α-helix	348-361	14

Chains C and G: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	9
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	9
β-strand	53-59	7	9
β-strand	62-70	9	9
β-strand	83-90	8	9
β-strand	95-97	3	9
α-helix	100-110	11
α-helix	162-164	3
α-helix	166-170	5

Chains D and H: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-14	6
α-helix	16-23	8
β-strand	27-28	2	9
α-helix	37-50	14
β-strand	55-59	5	9
β-strand	64-70	7	9
α-helix	71-73	3
β-strand	85-87	3	9
β-strand	94-103	10	9
β-strand	106-115	10	9
β-strand	120-127	8	9
α-helix	140-150	11

Chain E: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	10
α-helix	15-30	16
β-strand	39-41	3	10
α-helix	43-45	3
β-strand	51-58	8	10
β-strand	63-72	10	10
β-strand	82-91	10	10
β-strand	94-97	4	10
α-helix	100-110	11
α-helix	166-170	5

Chain F: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-20	5
β-strand	26-29	4	10
α-helix	37-50	14
β-strand	55-59	5	10
β-strand	64-69	6	10
α-helix	71-73	3
β-strand	85-87	3	10
β-strand	94-103	10	10
β-strand	106-115	10	10
β-strand	120-127	8	10
α-helix	139-149	11

Chain I: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	12
β-strand	11-13	3	12
α-helix	15-30	16
β-strand	39-41	3	12
α-helix	43-45	3
β-strand	51-58	8	12
β-strand	63-72	10	12
β-strand	82-91	10	12
β-strand	94-97	4	12
α-helix	100-110	11
α-helix	166-170	5

Chain J: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	16-20	5
β-strand	26-29	4	12
α-helix	37-50	14
β-strand	55-59	5	12
β-strand	65-69	5	12
α-helix	71-73	3
β-strand	85-87	3	12
β-strand	94-103	10	12
β-strand	106-115	10	12
β-strand	120-127	8	12
α-helix	139-149	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
APOBEC3G	A, B	protein	371	Homo sapiens	Q9HC16 (AlphaFold model)
Viral infectivity factor	C, E, G, I	protein	152	Human immunodeficiency virus 1	P12504
Core binding factor beta	D, F, H, J	protein	156	Homo sapiens	Q13951 (AlphaFold model)
RNA (5'-r(cpgpgpupupgpapupcpgpupupupupapapcpap*a)-3')	X, Y	RNA	20	synthetic construct

Sequence of entity 1 (A, B), FASTA

>8H0I_1 APOBEC3G (chains A, B)
GPGHMDPDTFSYNFNNRPILSRRNTVWLCYEVERLDNGTWVKMDQHRGQVYSELKYHPEM
RFLSLVSKWKLHRDQEYEVTWYISWSPCTKCARDMATFLQENTHVTLTIFVARLYYFWDP
DYQEALRSLAQAGATIKIMNYDEFQHCWSKFVYSQGAPFQPWDGLDEYSQALSGMLGEIL
RHSMDPPTFTFNFNNEPWVRGRHETYLCYEVERMHNDTWVKLNQRRGFLANQAPHKHGFL
EGRHAELCFLDVIPFWKLDLDQDYRVTCFTSWSPCFSCAQEMAKFISKNKHVSLCIKTAR
IYDDQGRAQEGLRTLAEAGAKISIMTYSEFKHCWDTFVDHQGAPFQPWDGLDEHSQDLSG
RLRAILQNQEN

Sequence of entity 2 (C, E, G, I), FASTA

>8H0I_2 Viral infectivity factor (chains C, E, G, I)
MGSSHHHHHHSQDPMENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYES
TNPKISSEVHIPLGDAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQL
IHLHYFDEASEGSQIKPPLPSVRKLTEDRWNK

Sequence of entity 3 (D, F, H, J), FASTA

>8H0I_3 Core binding factor beta (chains D, F, H, J)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDR

Sequence of entity 4 (X, Y), FASTA

>8H0I_4 RNA (5'-R(*CP*GP*GP*UP*UP*GP*AP*UP*CP*GP*UP*UP*UP*UP*AP*AP*CP*AP*A)-3') (chains X, Y)
CGGUUGAUCGUUUUAACAAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

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

Primary citation

Structural insights into RNA bridging between HIV-1 Vif and antiviral factor APOBEC3G. Kouno, T., Shibata, S., Shigematsu, M. et al. Nat Commun (2023) 14:4037-4037. DOI 10.1038/s41467-023-39796-5 · 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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