9CNT: Capsid protein p24

HIV-2 CA pentamer; assembled via liposome templating. Determined by electron microscopy at 2.97 Å resolution. Released 5 Mar 2025.

Method: Electron microscopy
Resolution: 2.97 Å
Organism: Human immunodeficiency virus 2
Chains: 4
Atoms: 7,016
Mol. weight: 108.56 kDa
Ligands: IHP
Released: 5 Mar 2025

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

Secondary structure: helices and β-sheets

9CNT contains 58 α-helices and 8 β-strands across 4 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: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	1
β-strand	9-12	4	1
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-58	10
α-helix	64-83	20
α-helix	90-91	2
α-helix	95-98	4
α-helix	100-104	5
α-helix	110-117	8
α-helix	126-145	20
α-helix	161-174	14
α-helix	179-187	9
α-helix	189-192	4
α-helix	196-204	9
α-helix	211-217	7

Chain B: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	2
β-strand	9-12	4	2
α-helix	14-16	3
α-helix	17-29	13
α-helix	36-43	8
α-helix	49-56	8
α-helix	63-83	21
α-helix	95-96	2
α-helix	101-104	4
α-helix	110-117	8
α-helix	126-145	20
α-helix	161-174	14
α-helix	179-192	14
α-helix	196-205	10
α-helix	211-217	7

Chain C: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	3
β-strand	12	1	3
α-helix	14-16	3
α-helix	17-29	13
α-helix	36-43	8
α-helix	49-58	10
α-helix	65-83	19
α-helix	90-91	2
α-helix	96-98	3
α-helix	100-104	5
α-helix	110-117	8
α-helix	126-145	20
α-helix	161-175	15
α-helix	179-192	14
α-helix	196-201	6
α-helix	211-217	7

Chain D: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	4
β-strand	9-12	4	4
α-helix	14-16	3
α-helix	17-29	13
α-helix	36-43	8
α-helix	49-58	10
α-helix	64-83	20
α-helix	95-98	4
α-helix	100-104	5
α-helix	110-117	8
α-helix	127-145	19
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-184	6
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-217	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein p24	A, B, C, D	protein	240	Human immunodeficiency virus 2	P18042

Sequence of entity 1 (A, B, C, D), FASTA

>9CNT_1 Capsid protein p24 (chains A, B, C, D)
PVQQTGGGNYIHVPLSPRTLNAWVKLVEDKKFGAEVVPGFQALSEGCTPYDINQMLNCVG
DHQAAMQIIREIINDEAADWDAQHPIPGPLPAGQLRDPRGSDIAGTTSTVEEQIQWMYRP
QNPVPVGNIYRRWIQIGLQKCVRMYNPTNILDVKQGPKEPFQSYVDRFYKSLRAEQTDPA
VKNWMTQTLLIQNANPDCKLVLKGLGMNPTLEEMLTACQGVGGPGQKARLMGSSHHHHHH

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
9CNU 2.99 Å, HIV-2 CA hexamer bound with Nup153 peptide; assembled with liposome templating
9CNV 3.16 Å, HIV-2 CA hexamer bound with CPSF6 peptide; assembled via 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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