9CNV: HIV-2 CA hexamer

HIV-2 CA hexamer bound with CPSF6 peptide; assembled via liposome templating. Determined by electron microscopy at 3.16 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 3.16 Å
Organisms: Human immunodeficiency virus 2, Homo sapiens
Chains: 2
Atoms: 1,898
Mol. weight: 29.68 kDa
Ligands: IHP
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9CNV contains 15 α-helices and 2 β-strands across 2 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: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	10-12	3	1
α-helix	14-16	3
α-helix	17-29	13
α-helix	36-43	8
α-helix	49-58	10
α-helix	63-83	21
α-helix	94-98	5
α-helix	100-104	5
α-helix	110-117	8
α-helix	126-145	20
α-helix	161-174	14
α-helix	179-185	7
α-helix	189-192	4
α-helix	198-203	6
α-helix	211-217	7

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	7-8	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein p24	A	protein	240	Human immunodeficiency virus 2	P18042
Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6	B	protein	15	Homo sapiens	Q16630 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9CNV_1 Capsid protein p24 (chains A)
PVQQTGGGNYIHVPLSPRTLNAWVKLVEDKKFGAEVVPGFQALSEGCTPYDINQMLNCVG
DHQAAMQIIREIINDEAADWDAQHPIPGPLPAGQLRDPRGSDIAGTTSTVEEQIQWMYRP
QNPVPVGNIYRRWIQIGLQKCVRMYNPTNILDVKQGPKEPFQSYVDRFYKSLRAEQTDPA
VKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTACQGVGGPGQKARLMGSSHHHHHH

Sequence of entity 2 (B), FASTA

>9CNV_2 Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6 (chains B)
PVLFPGQPFGQPPLG

Ligands and cofactors

ID	Name	Formula	Copies
IHP	Inositol hexakisphosphate	C6 H18 O24 P6	2

Primary citation

Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM. Cook, M., Freniere, C., Wu, C. et al. Cell Rep (2025) 44:115245-115245. DOI 10.1016/j.celrep.2025.115245 · PubMed

Other PDB entries of the same protein (UniProt P18042), best resolution first:

9CLJ 1.98 Å, HIV-2 CA T=1 Icosahedron; assembled via lipid templating
9CNT 2.97 Å, HIV-2 CA pentamer; assembled via liposome templating
9CNU 2.99 Å, HIV-2 CA hexamer bound with Nup153 peptide; assembled with liposome templating
9CNS 3.25 Å, HIV-2 CA hexamer; assembled via liposome templating
2E1X NMR structure of the HIV-2 nucleocapsid protein
2IWJ Solution structure of the ZN complex of HIV-2 NCP(23-49) peptide, encompassing protein…

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