7RMJ: Disulfide stabilized HIV-1 CA hexamer

Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor (S)-N-(1-(3-(4-chloro-3-(methylsulfonamido)-1-(2,2,2-trifluoroethyl)-1H-indazol-7-yl)-6-(3-methyl-3-(methylsulfonyl)but-1-yn-1-yl)pyridin-2-yl)-2-(3,5-difluorophenyl)ethyl)-2-(3-(trifluoromethyl)-4,5,6,7-tetrahydro-1H-indazol-1-…. Determined by X-ray diffraction at 2.27 Å resolution. Released 3 Aug 2022.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Human immunodeficiency virus 1
Chains: 3
Atoms: 5,698
Mol. weight: 80.42 kDa
Ligands: 61F
Released: 3 Aug 2022

Explore 7RMJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RMJ contains 48 α-helices and 6 β-strands across 3 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: 16 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	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	90-92	3
α-helix	97-100	4
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-185	7
α-helix	186-190	5
α-helix	196-205	10
α-helix	211-217	7

Chain B: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	10-12	3	2
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	90-92	3
α-helix	97-99	3
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
α-helix	150-152	3
α-helix	161-174	14
α-helix	182-184	3
α-helix	185-189	5
α-helix	190-192	3
α-helix	196-205	10
α-helix	211-217	7

Chain C: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	3
β-strand	10-12	3	3
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-43	8
α-helix	49-57	9
α-helix	63-83	21
α-helix	90-92	3
α-helix	97-99	3
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-189	11
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	protein	231	Human immunodeficiency virus 1	B6DRA0

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

>7RMJ_1 CAPSID PROTEIN P24 (chains A, B, C)
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Ligands and cofactors

ID	Name	Formula	Copies
61F	N-[(1S)-1-(3-{4-chloro-3-[(methanesulfonyl)amino]-1-(2,2,2-trifluoroethyl)-1H-i…	C39 H36 Cl F8 N7 O5 S2	3

Water and common crystallization additives (IOD, CL) are not listed.

Primary citation

Structural and Mechanistic Bases of Viral Resistance to HIV-1 Capsid Inhibitor Lenacapavir. Bester, S.M., Adu-Ampratwum, D., Annamalai, A.S. et al. mBio (2022) 13:e0180422-e0180422. DOI 10.1128/mbio.01804-22 · PubMed

Other PDB entries of the same protein (UniProt B6DRA0), best resolution first:

6R8C 1.92 Å, HIV capsid hexamer with IP5 ligand
9RPC 1.97 Å, HIV-1 capsid (M-group) - native
7RMM 1.97 Å, Structure of N74D mutant of disulfide stabilized HIV-1 CA hexamer
6ERM 2.0 Å, HIV Hexamer with ligand
9S6W 2.07 Å, HIV-1 capsid (M-group) - native in complex with JW3-100
9S6O 2.09 Å, HIV-1 capsid (M-group) - native in complex with JW3-076
9PGT 2.2 Å, HIV Capsid Hexamer bound to Compound 12
9PGV 2.3 Å, HIV Capsid Hexamer bound to Compound 24
6ERN 2.36 Å, HIV Hexamer with ligand
9S6V 2.36 Å, HIV-1 capsid (M-group) - native in complex with JW3-094
9PGS 2.4 Å, HIV Capsid Hexamer bound to Compound 6
9S6J 2.4 Å, HIV-1 capsid (M-group) - CPSF6

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