1AFV: HIV-1 capsid protein (P24) complex with FAB25.3

HIV-1 capsid protein (P24) complex with FAB25.3. Determined by X-ray diffraction at 3.7 Å resolution. Released 20 Aug 1997.

Method: X-ray diffraction
Resolution: 3.7 Å
Organisms: Human immunodeficiency virus 1, Mus musculus
Chains: 6
Atoms: 9,024
Mol. weight: 128.73 kDa
Ligands: PB
Released: 20 Aug 1997

Explore 1AFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1AFV contains 47 α-helices and 91 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 A and B: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	14-16	3
α-helix	17-30	14
α-helix	36-42	7
α-helix	49-58	10
α-helix	63-82	20
α-helix	86-88	3
α-helix	98-100	3
α-helix	101-104	4
α-helix	111-117	7
α-helix	126-143	18

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	7
β-strand	9-12	4	8
β-strand	18-20	3	7
β-strand	23-25	3	7
α-helix	29-31	3
β-strand	33-39	7	8
β-strand	45-51	7	8
β-strand	58-60	3	8
α-helix	62-64	3
β-strand	68-73	6	7
α-helix	74-76	3
β-strand	78-83	6	7
α-helix	88-90	3
β-strand	93-99	7	8
β-strand	107-110	4	8
β-strand	114-118	5	8
β-strand	124	1	9
β-strand	127-131	5	10
β-strand	142-152	11	10
β-strand	153	1	9
β-strand	158-161	4	11
α-helix	162-164	3
β-strand	171-172	2	10
α-helix	173-175	3
β-strand	176-177	2	10
β-strand	182-191	10	10
α-helix	195-197	3
β-strand	201-206	6	11
α-helix	207-209	3
β-strand	211-216	6	11

Chain K: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	19
β-strand	9-12	4	20
β-strand	18-20	3	19
β-strand	23-25	3	19
α-helix	29-31	3
β-strand	33-39	7	20
α-helix	45	1
β-strand	46-51	6	20
β-strand	58-60	3	20
β-strand	68-73	6	19
α-helix	74-76	3
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	93-99	7	20
β-strand	107-110	4	20
β-strand	114-118	5	20
α-helix	121-123	3
β-strand	124	1	21
β-strand	127-131	5	22
β-strand	143-152	10	22
β-strand	153	1	21
β-strand	158-161	4	23
α-helix	162-164	3
β-strand	171-172	2	22
α-helix	173-175	3
β-strand	176-177	2	22
β-strand	182-190	9	22
α-helix	195-197	3
β-strand	201-206	6	23
α-helix	207-209	3
β-strand	211-216	6	23

Chain L: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	30	1	3
β-strand	35	1	3
β-strand	37-42	6	2
β-strand	49-53	5	2
β-strand	57-58	2	2
β-strand	66-71	6	1
β-strand	74-79	6	1
α-helix	84-86	3
β-strand	88-94	7	2
β-strand	101-102	2	2
β-strand	106-111	6	2
α-helix	112-114	3
β-strand	115	1	4
β-strand	118-122	5	5
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	5
β-strand	144	1	4
β-strand	149-154	6	6
β-strand	157-159	3	6
β-strand	163-167	5	5
β-strand	177-186	10	5
α-helix	187-191	5
β-strand	195-202	8	6
β-strand	205-214	10	6

Chain M: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	30	1	14
β-strand	35	1	14
β-strand	37-42	6	13
β-strand	49-53	5	13
β-strand	57-58	2	13
β-strand	66-71	6	12
β-strand	74-79	6	12
α-helix	84-86	3
β-strand	88-94	7	13
β-strand	101-102	2	13
β-strand	106-111	6	13
α-helix	112-114	3
β-strand	115	1	15
β-strand	118-122	5	16
α-helix	123-125	3
α-helix	126-130	5
β-strand	133-143	11	16
β-strand	144	1	15
β-strand	149-152	4	17
β-strand	154	1	18
β-strand	157	1	18
β-strand	163-167	5	16
β-strand	177-186	10	16
α-helix	187-191	5
β-strand	195-202	8	17
β-strand	205-214	10	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human immunodeficiency virus type 1 capsid protein	A, B	protein	151	Human immunodeficiency virus 1	P12497
Antibody FAB25.3 fragment (light chain)	L, M	protein	217	Mus musculus
Antibody FAB25.3 fragment (heavy chain)	H, K	protein	220	Mus musculus	Q99LC4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1AFV_1 HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 CAPSID PROTEIN (chains A, B)
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSIL

Sequence of entity 2 (L, M), FASTA

>1AFV_2 ANTIBODY FAB25.3 FRAGMENT (LIGHT CHAIN) (chains L, M)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGISFMNWFQQKPGQPPKLLIYAASNLGS
GVPARFSGSGSGTDFSLNIHPMEEEDTAMYFCQQSKEVPLTFGAGTKVELKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Sequence of entity 3 (H, K), FASTA

>1AFV_3 ANTIBODY FAB25.3 FRAGMENT (HEAVY CHAIN) (chains H, K)
QVQLQQPGSVLVRPGASVKLSCKASGYTFTSSWIHWAKQRPGQGLEWIGEIHPNSGNTNY
NEKFKGKATLTVDTSSSTAYVDLSSLTSEDSAVYYCARWRYGSPYYFDYWGQGTTLTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPK

Ligands and cofactors

ID	Name	Formula	Copies
PB	Lead (II) ion	Pb	2

Primary citation

Crystal structure of dimeric HIV-1 capsid protein. Momany, C., Kovari, L.C., Prongay, A.J. et al. Nat Struct Biol (1996) 3:763-770. DOI 10.1038/nsb0996-763 · PubMed

Other PDB entries of the same protein (UniProt P12497), best resolution first:

3DS4 1.12 Å, HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle…
3DS2 1.2 Å, HIV-1 capsid C-terminal domain mutant (Y169A)
6T6E 1.3 Å, Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3)
2XDE 1.4 Å, Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal…
3L3U 1.4 Å, Crystal structure of the HIV-1 integrase core domain to 1.4A
2PWO 1.45 Å, Crystal Structure of HIV-1 CA146 A92E Psuedo Cell
3WNF 1.45 Å, Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
6MCR 1.48 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
2PXR 1.5 Å, Crystal Structure of HIV-1 CA146 in the Presence of CAP-1
3WNH 1.5 Å, Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase
4NX4 1.5 Å, Re-refinement of CAP-1 HIV-CA complex

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