9ZY1: Dimeric HIV-2 Vif-human APOBEC3H-CBFbeta complex

Cryo-EM structure of the dimeric HIV-2 Vif-human APOBEC3H-CBFbeta complex. Determined by electron microscopy at 3.2 Å resolution. Released 15 Jul 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Human immunodeficiency virus 2, Homo sapiens, synthetic construct
Chains: 8
Atoms: 8,774
Mol. weight: 141.82 kDa
Ligands: ZN
Released: 15 Jul 2026

Explore 9ZY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9ZY1 contains 52 α-helices and 46 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.

Chains 1 and A: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-6	4
β-strand	7-15	9	1
α-helix	20-27	8
α-helix	28-33	6
β-strand	40-42	3	1
α-helix	44-46	3
β-strand	50	1	2
β-strand	56-61	6	1
β-strand	65-72	8	1
α-helix	83-84	2
β-strand	85-92	8	1
β-strand	97-99	3	1
α-helix	102-109	8
α-helix	119-127	9
α-helix	129-131	3
α-helix	138-141	4
α-helix	148-159	12
α-helix	207-210	4

Chains 2 and B: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-14	9
α-helix	16-22	7
β-strand	25-28	4	1
α-helix	37-49	13
β-strand	55-59	5	1
β-strand	64-70	7	1
β-strand	74	1	2
β-strand	82	1	1
α-helix	83-85	3
β-strand	86-87	2	1
β-strand	94-103	10	1
β-strand	106-115	10	1
β-strand	120-127	8	1
α-helix	129-134	6
α-helix	137-148	12

Chains 3 and C: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	3
α-helix	6-12	7
α-helix	19-20	2
α-helix	23	1
β-strand	30-36	7	4
α-helix	40-42	3
β-strand	43-47	5	4
α-helix	55-66	12
β-strand	74-82	9	4
α-helix	86-98	13
β-strand	102-110	9	4
α-helix	117-128	12
β-strand	133	1	4
α-helix	138-147	10
β-strand	149	1	3
α-helix	159-182	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Virion infectivity factor	1, A	protein	215	Human immunodeficiency virus 2	Q9YTT9
Core-binding factor subunit beta	2, B	protein	182	Homo sapiens	Q13951 (AlphaFold model)
Single-stranded DNA cytosine deaminase	3, C	protein	183	Homo sapiens	B7TQM6 (AlphaFold model)
RNA (5'-r(pupupupupupupupu)-3')	D	RNA	8	synthetic construct
RNA (5'-r(papapapapapapapa)-3')	E	RNA	8	synthetic construct

Sequence of entity 1 (1, A), FASTA

>9ZY1_1 Virion infectivity factor (chains 1, A)
MEEGKSWIVVPTWRVPGRMEKWHSLVKYLKYRTKDLEKVCYVPHHKVGWAWWTCSRVIFP
LQGRSHLEIQAYWNLTPEKGWLSSYAVRITWYTEKFWTDVTPDCADSLIHGTYFSCFTAG
EVRRAIRGEKLLSCCNYPQAHKSQVPSLQFLALVVVQQNGKPQRNSTTRKQWRRDYRRGL
RVARQDSRGLKQRGGESPAPGAHFPGVAKVLEILA

Sequence of entity 2 (2, B), FASTA

>9ZY1_2 Core-binding factor subunit beta (chains 2, B)
MPRVVPDQRSKFENEEFFRKLSRECEIKYTGFRDRPHEERQARFQNACRDGRSEIAFVAT
GTNLSLQFFPASWQGEQRQTPSREYVDLEREAGKVYLKAPMILNGVCVIWKGWIDLQRLD
GMGCLEFDEERAQQEDALAQQAFEEARRRTREFEDRDRSHREEMEVRVSQLLAVTGKKTT
RP

Sequence of entity 3 (3, C), FASTA

>9ZY1_3 Single-stranded DNA cytosine deaminase (chains 3, C)
MALLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEICFI
NEIKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIKAHDHLNLRIFASRLYYHWCKPQQ
DGLRLLCGSQVPVEVMGFPEFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLDRI
KQS

Sequence of entity 4 (D), FASTA

>9ZY1_4 RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3') (chains D)
UUUUUUUU

Sequence of entity 5 (E), FASTA

>9ZY1_5 RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*A)-3') (chains E)
AAAAAAAA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

The structural mechanism of HIV-2 Vif antagonism of human APOBEC3H. Niu, Y., Lilly, M., Ronayne, E.K. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-75045-1 · PubMed

Other PDB entries of the same protein (UniProt Q9YTT9), best resolution first:

9ZY0 3.2 Å, Cryo-EM structure of the monomeric HIV-2 Vif-human APOBEC3H-CBFbeta complex

Browse structure collections

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