SMTL ID : 9cnv.1 (1 other biounit)

HIV-2 CA hexamer bound with CPSF6 peptide; assembled via liposome templating

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

12 x IHP: INOSITOL HEXAKISPHOSPHATE(Non-covalent)

IHP.1: 19 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: S.16, R.18 Chain K: S.16, R.18 Ligands: IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 13 PLIP interactions: 2 interactions with chain K, 2 interactions with chain E, 3 interactions with chain I, 3 interactions with chain G, 1 interactions with chain C, 2 interactions with chain A Hydrogen bonds: K:S.16, E:R.18, I:S.16, G:R.18 Salt bridges: K:R.18, E:R.18, I:R.18, I:R.18, G:R.18, G:R.18, C:R.18, A:R.18, A:R.18 IHP.2: 17 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 10 PLIP interactions: 1 interactions with chain C, 2 interactions with chain K, 2 interactions with chain A, 2 interactions with chain G, 2 interactions with chain E, 1 interactions with chain I Salt bridges: C:R.18, K:R.18, K:R.18, A:R.18, A:R.18, G:R.18, E:R.18, E:R.18 Hydrogen bonds: G:R.18, I:R.18 IHP.3: 19 residues within 4Å: Chain A: S.16, R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: S.16, R.18 Ligands: IHP.1, IHP.2, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 13 PLIP interactions: 3 interactions with chain K, 1 interactions with chain E, 3 interactions with chain I, 2 interactions with chain G, 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: K:S.16, I:R.18, G:R.18, A:S.16 Salt bridges: K:R.18, K:R.18, E:R.18, I:R.18, I:R.18, G:R.18, A:R.18, C:R.18, C:R.18 IHP.4: 17 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 10 PLIP interactions: 2 interactions with chain C, 1 interactions with chain K, 2 interactions with chain A, 2 interactions with chain G, 1 interactions with chain E, 2 interactions with chain I Salt bridges: C:R.18, C:R.18, A:R.18, A:R.18, G:R.18, G:R.18, E:R.18, I:R.18 Hydrogen bonds: K:R.18, I:R.18 IHP.5: 19 residues within 4Å: Chain A: S.16, R.18 Chain C: S.16, R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 13 PLIP interactions: 3 interactions with chain K, 2 interactions with chain C, 2 interactions with chain E, 2 interactions with chain I, 1 interactions with chain G, 3 interactions with chain A Hydrogen bonds: K:R.18, C:S.16, I:R.18, A:S.16 Salt bridges: K:R.18, K:R.18, C:R.18, E:R.18, E:R.18, I:R.18, G:R.18, A:R.18, A:R.18 IHP.6: 17 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 10 PLIP interactions: 2 interactions with chain C, 2 interactions with chain K, 1 interactions with chain A, 1 interactions with chain G, 2 interactions with chain E, 2 interactions with chain I Salt bridges: C:R.18, C:R.18, K:R.18, G:R.18, E:R.18, E:R.18, I:R.18, I:R.18 Hydrogen bonds: K:R.18, A:R.18 IHP.7: 19 residues within 4Å: Chain A: R.18 Chain C: S.16, R.18 Chain E: S.16, R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.8, IHP.9, IHP.10, IHP.11, IHP.12 13 PLIP interactions: 2 interactions with chain K, 3 interactions with chain C, 2 interactions with chain E, 1 interactions with chain I, 2 interactions with chain G, 3 interactions with chain A Hydrogen bonds: K:R.18, C:S.16, E:S.16, A:R.18 Salt bridges: K:R.18, C:R.18, C:R.18, E:R.18, I:R.18, G:R.18, G:R.18, A:R.18, A:R.18 IHP.8: 17 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.9, IHP.10, IHP.11, IHP.12 10 PLIP interactions: 1 interactions with chain C, 2 interactions with chain K, 2 interactions with chain A, 2 interactions with chain G, 2 interactions with chain E, 1 interactions with chain I Hydrogen bonds: C:R.18, A:R.18 Salt bridges: K:R.18, K:R.18, A:R.18, G:R.18, G:R.18, E:R.18, E:R.18, I:R.18 IHP.9: 19 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: S.16, R.18 Chain G: S.16, R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.10, IHP.11, IHP.12 13 PLIP interactions: 1 interactions with chain K, 2 interactions with chain G, 3 interactions with chain E, 2 interactions with chain I, 3 interactions with chain C, 2 interactions with chain A Salt bridges: K:R.18, G:R.18, E:R.18, E:R.18, I:R.18, I:R.18, C:R.18, C:R.18, A:R.18 Hydrogen bonds: G:S.16, E:S.16, C:R.18, A:R.18 IHP.10: 17 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.11, IHP.12 10 PLIP interactions: 2 interactions with chain C, 1 interactions with chain K, 2 interactions with chain A, 2 interactions with chain G, 1 interactions with chain E, 2 interactions with chain I Hydrogen bonds: C:R.18, E:R.18 Salt bridges: C:R.18, K:R.18, A:R.18, A:R.18, G:R.18, G:R.18, I:R.18, I:R.18 IHP.11: 19 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: S.16, R.18 Chain I: S.16, R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.12 13 PLIP interactions: 2 interactions with chain K, 3 interactions with chain G, 3 interactions with chain E, 2 interactions with chain I, 2 interactions with chain C, 1 interactions with chain A Salt bridges: K:R.18, K:R.18, G:R.18, G:R.18, E:R.18, E:R.18, I:R.18, C:R.18, A:R.18 Hydrogen bonds: G:S.16, E:R.18, I:S.16, C:R.18 IHP.12: 17 residues within 4Å: Chain A: R.18 Chain C: R.18 Chain E: R.18 Chain G: R.18 Chain I: R.18 Chain K: R.18 Ligands: IHP.1, IHP.2, IHP.3, IHP.4, IHP.5, IHP.6, IHP.7, IHP.8, IHP.9, IHP.10, IHP.11 10 PLIP interactions: 2 interactions with chain C, 2 interactions with chain K, 1 interactions with chain A, 1 interactions with chain G, 2 interactions with chain E, 2 interactions with chain I Salt bridges: C:R.18, C:R.18, K:R.18, K:R.18, A:R.18, E:R.18, I:R.18, I:R.18 Hydrogen bonds: G:R.18, E:R.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cook, M. et al., Structural insights into HIV-2 CA lattice formation and FG-pocket binding revealed by single-particle cryo-EM. Cell Rep (2025)

Release Date

2025-03-05

Peptides

Capsid protein p24: ACEGIK
Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
B

D
B

F
B

H
B

J
B

L
B

Capsid protein p24

Isoform 2 of Cleavage and polyadenylation specificity factor subunit 6

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