9E9V: Single-stranded DNA cytosine deaminase

Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H. Determined by electron microscopy at 4.0 Å resolution. Released 11 Mar 2026.

Method: Electron microscopy
Resolution: 4.0 Å
Organisms: Pan troglodytes, Escherichia coli BL21(DE3), Homo sapiens
Chains: 13
Atoms: 10,935
Mol. weight: 182.5 kDa
Ligands: ZN
Released: 11 Mar 2026

Explore 9E9V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E9V contains 57 α-helices and 69 β-strands across 9 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: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	30-36	7	1
β-strand	43	1	1
β-strand	46-47	2	1
β-strand	50	1	2
β-strand	53	1	2
α-helix	55-65	11
β-strand	74-82	9	1
α-helix	83-85	3
α-helix	86-98	13
β-strand	103-105	3	1
β-strand	106	1	3
β-strand	108-110	3	1
α-helix	117-128	12
β-strand	133	1	3
α-helix	138-147	10
α-helix	159-169	11
α-helix	174-181	8

Chain B: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	19-20	2
β-strand	30-34	5	4
α-helix	40-42	3
β-strand	43-47	5	4
β-strand	50	1	5
β-strand	53	1	5
α-helix	55-65	11
β-strand	75-80	6	4
α-helix	83-85	3
α-helix	86-98	13
β-strand	103-104	2	4
β-strand	106	1	6
β-strand	108	1	4
α-helix	117-128	12
β-strand	133	1	6
α-helix	138-148	11
α-helix	159-182	24

Chain E: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	8-11	4
β-strand	30-31	2	7
β-strand	34-35	2	7
α-helix	41-43	3
β-strand	46-47	2	7
β-strand	50	1	8
β-strand	53	1	8
α-helix	55-65	11
β-strand	74-82	9	7
α-helix	83-85	3
α-helix	86-98	13
β-strand	102-110	9	7
α-helix	117-128	12
β-strand	133-134	2	7
α-helix	138-142	5
α-helix	143-148	6
α-helix	154-155	2
α-helix	160-181	22

Chain m: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
β-strand	12-18	7	9
α-helix	24-34	11
β-strand	44-46	3	10
β-strand	49-50	2	10
α-helix	51-52	2
α-helix	58-60	3
β-strand	73-75	3	9
β-strand	76-77	2	10
α-helix	91-94	4

Chain n: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	9
β-strand	28-32	5	9
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	9
α-helix	67-83	17
α-helix	97-110	14

Chain o: 5 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-23	8
β-strand	27	1	13
α-helix	37-49	13
β-strand	55	1	11
β-strand	58	1	11
β-strand	59	1	13
β-strand	64-70	7	11
β-strand	85	1	14
β-strand	98	1	14
β-strand	99-103	5	12
β-strand	106-111	6	12
β-strand	124-127	4	12
α-helix	130-134	5
α-helix	137-148	12

Chain p: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	11
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	11
β-strand	51-59	9	11
β-strand	62-69	8	11
β-strand	83-91	9	11
β-strand	94-96	3	11
β-strand	97	1	12
α-helix	100-111	12
α-helix	119-125	7
α-helix	127-129	3
α-helix	136-138	3
α-helix	145-153	9
α-helix	162-164	3
α-helix	166-169	4

Chain s: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	16-23	8
β-strand	28	1	17
α-helix	37-49	13
β-strand	56	1	15
β-strand	58	1	17
β-strand	64-70	7	15
β-strand	86-91	6	16
β-strand	94-98	5	16
β-strand	101-103	3	16
β-strand	106-114	9	16
β-strand	123-127	5	16
α-helix	130-134	5
α-helix	137-145	9

1 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
single-stranded DNA cytosine deaminase	A, B, E	protein	183	Pan troglodytes	B7T0U6 (AlphaFold model)
RNA (5'-r(pcpcpcpgpgpcp*a)-3')	D, H	RNA	10	Escherichia coli BL21(DE3)
RNA (5'-r(pgpcpcpgpgpg)-3')	C, G	RNA	9	Escherichia coli BL21(DE3)
Elongin-C	n	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Elongin-B	m	protein	102	Homo sapiens	Q15370 (AlphaFold model)
Virion infectivity factor	p, t	protein	176	Human immunodeficiency virus 1	P12504
Core-binding factor subunit beta	o, s	protein	170	Homo sapiens	Q13951

Sequence of entity 1 (A, B, E), FASTA

>9E9V_1 single-stranded DNA cytosine deaminase (chains A, B, E)
MALLTAETFRLQFNNRRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFI
NEIKSMGLDETQCYQVTCYLTWSPCSSCAWKLVDFIQAHDHLNLRIFASRLYYHWCKPQQ
EGLRLLCGSQVPVEVMGLPEFNDCWENFVDHEKPLSFDPCKMLEELDKNSRAIKRRLERI
KQS

Sequence of entity 2 (D, H), FASTA

>9E9V_2 RNA (5'-R(P*CP*CP*CP*GP*GP*CP*A)-3') (chains D, H)
AUACCCGGCA

Sequence of entity 3 (C, G), FASTA

>9E9V_3 RNA (5'-R(P*GP*CP*CP*GP*GP*G)-3') (chains C, G)
UGCCGGGUA

Sequence of entity 4 (n), FASTA

>9E9V_4 Elongin-C (chains n)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 5 (m), FASTA

>9E9V_5 Elongin-B (chains m)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDV

Sequence of entity 6 (p, t), FASTA

>9E9V_6 Virion infectivity factor (chains p, t)
MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLG
DAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAI
RNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

Sequence of entity 7 (o, s), FASTA

>9E9V_7 Core-binding factor subunit beta (chains o, s)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

HIV-1 vif mediates ubiquitination of the proximal protomer in the APOBEC3H dimer to induce degradation. Skorupka, K.A., Matsuoka, K., Hassan, B. et al. Nat Commun (2025) 16:5879-5879. DOI 10.1038/s41467-025-60984-y · PubMed

Other PDB entries of the same protein (UniProt B7T0U6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5Z98 2.2 Å, Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex
9E93 3.58 Å, Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

Browse structure collections

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