9E93: Single-stranded DNA cytosine deaminase

Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H. Determined by electron microscopy at 3.58 Å resolution. Released 11 Mar 2026.

Method: Electron microscopy
Resolution: 3.58 Å
Organisms: Escherichia coli BL21(DE3), Pan troglodytes, Homo sapiens
Chains: 10
Atoms: 8,773
Mol. weight: 138.69 kDa
Ligands: ZN
Released: 11 Mar 2026

Explore 9E93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E93 contains 47 α-helices and 45 β-strands across 6 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: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	19-20	2
α-helix	23	1
β-strand	29-36	8	1
β-strand	44-48	5	1
β-strand	50	1	2
β-strand	53	1	2
α-helix	55-65	11
β-strand	74-79	6	1
β-strand	80-82	3	3
α-helix	83-85	3
α-helix	86-98	13
β-strand	102-105	4	1
β-strand	106	1	4
β-strand	108-110	3	3
α-helix	117-128	12
β-strand	133	1	4
α-helix	138-146	9
α-helix	154-155	2
α-helix	159-181	23

Chain E: 8 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
β-strand	30-36	7	5
α-helix	40-42	3
β-strand	45-46	2	5
β-strand	50	1	6
β-strand	53	1	6
α-helix	55-65	11
β-strand	74-82	9	5
α-helix	83-85	3
α-helix	86-98	13
β-strand	102-110	9	5
α-helix	117-128	12
β-strand	133-134	2	5
α-helix	138-148	11
α-helix	159-181	23

Chain o: 5 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-14	7
α-helix	16-23	8
β-strand	27-28	2	7
α-helix	37-49	13
β-strand	55	1	7
β-strand	58-59	2	7
β-strand	64-70	7	7
β-strand	86-87	2	7
β-strand	94-103	10	7
β-strand	106-115	10	7
β-strand	120-121	2	7
β-strand	124-127	4	7
α-helix	130-134	5
α-helix	137-148	12

Chain p: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	7
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	7
β-strand	51-59	9	7
β-strand	62-69	8	7
β-strand	83-91	9	7
β-strand	94-97	4	7
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	155-157	3
α-helix	162-164	3
α-helix	166-169	4

Chain s: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	8-12	5
α-helix	16-23	8
β-strand	27-28	2	8
α-helix	37-49	13
β-strand	56-58	3	8
β-strand	64-70	7	8
β-strand	85-87	3	8
β-strand	94-103	10	8
β-strand	106-115	10	8
β-strand	120-127	8	8
α-helix	130-134	5
α-helix	137-146	10

Chain t: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	5-13	9	8
α-helix	15-26	12
α-helix	27-31	5
β-strand	39-41	3	8
β-strand	51-59	9	8
β-strand	62-70	9	8
β-strand	83-91	9	8
β-strand	94-97	4	8
α-helix	100-109	10
α-helix	119-124	6
α-helix	142-144	3
α-helix	147-153	7
α-helix	155-156	2
α-helix	162-164	3
α-helix	166-170	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA (5'-r(pupgpcpcpgpgpgpup*a)-3')	C, G	RNA	9	Escherichia coli BL21(DE3)
RNA (5'-r(apupapcpcpcpgpgpcpa)-3')	D, H	RNA	10	Escherichia coli BL21(DE3)
single-stranded DNA cytosine deaminase	A, E	protein	185	Pan troglodytes	B7T0U6 (AlphaFold model)
Core-binding factor subunit beta	o, s	protein	170	Homo sapiens	Q13951 (AlphaFold model)
Virion infectivity factor	p, t	protein	176	Human immunodeficiency virus 1	P12504

Sequence of entity 1 (C, G), FASTA

>9E93_1 RNA (5'-R(P*UP*GP*CP*CP*GP*GP*GP*UP*A)-3') (chains C, G)
UGCCGGGUA

Sequence of entity 2 (D, H), FASTA

>9E93_2 RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3') (chains D, H)
AUACCCGGCA

Sequence of entity 3 (A, E), FASTA

>9E93_3 single-stranded DNA cytosine deaminase (chains A, E)
GSMALLTAETFRLQFNNRRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEIC
FINEIKSMGLDETQCYQVTCYLTWSPCSSCAWKLVDFIQAHDHLNLRIFASRLYYHWCKP
QQEGLRLLCGSQVPVEVMGLPEFNDCWENFVDHEKPLSFDPCKMLEELDKNSRAIKRRLE
RIKQS

Sequence of entity 4 (o, s), FASTA

>9E93_4 Core-binding factor subunit beta (chains o, s)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQ

Sequence of entity 5 (p, t), FASTA

>9E93_5 Virion infectivity factor (chains p, t)
MENRWQVMIVWQVDRMRINTWKRLVKHHMYISRKAKDWFYRHHYESTNPKISSEVHIPLG
DAKLVITTYWGLHTGERDWHLGQGVSIEWRKKRYSTQVDPDLADQLIHLHYFDCFSESAI
RNTILGRIVSPRCEYQAGHNKVGSLQYLALAALIKPKQIKPPLPSVRKLTEDRWNK

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
9E9V 4.0 Å, Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

Browse structure collections

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