3VRL: BMJ4 p24 capsid protein

Crystal structure of BMJ4 p24 capsid protein in complex with A10F9 Fab. Determined by X-ray diffraction at 3.2 Å resolution. Released 17 Apr 2013.

Method: X-ray diffraction
Resolution: 3.2 Å
Organisms: Mus musculus, Human immunodeficiency virus 1
Chains: 6
Atoms: 7,806
Mol. weight: 146.52 kDa
Released: 17 Apr 2013

Explore 3VRL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3VRL contains 37 α-helices and 83 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.

Chain C: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-192	14
α-helix	196-204	9
α-helix	211-218	8

Chain D: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	150-152	3
α-helix	161-174	14
α-helix	179-193	15
α-helix	196-204	9
α-helix	211-217	7

Chain E: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	34-39	6	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	65	1	10
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	109-112	4	12
β-strand	116-118	3	12
β-strand	119-120	2	11
α-helix	123-125	3
β-strand	129-133	5	13
β-strand	144-154	11	13
β-strand	160-163	4	14
α-helix	164-166	3
β-strand	172-174	3	13
α-helix	175-177	3
β-strand	178-179	2	13
β-strand	184-193	10	13
α-helix	196-199	4
β-strand	203-208	6	14
α-helix	209-211	3
β-strand	213-218	6	14

Chain F: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	15
β-strand	10-13	4	16
β-strand	19-25	7	15
β-strand	33-38	6	16
β-strand	45-49	5	16
β-strand	53-54	2	16
α-helix	55	1
β-strand	62	1	15
β-strand	65-66	2	15
β-strand	70-75	6	15
α-helix	80-82	3
β-strand	84-90	7	16
α-helix	97	1
β-strand	98	1	16
α-helix	99	1
β-strand	102-106	5	16
β-strand	111	1	17
β-strand	114-118	5	18
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	18
β-strand	140	1	17
β-strand	145-150	6	19
β-strand	153-155	3	19
β-strand	159-163	5	18
β-strand	173-182	10	18
α-helix	183-186	4
β-strand	191-197	7	19
β-strand	205-210	6	19

Chain H: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	10-12	3	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	34-39	6	2
β-strand	45-51	7	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-98	7	2
β-strand	111-112	2	2
β-strand	116-120	5	2
β-strand	126	1	3
β-strand	129-133	5	4
β-strand	144-154	11	4
β-strand	155	1	3
β-strand	160-163	4	5
α-helix	164-166	3
β-strand	172-174	3	4
α-helix	175-177	3
β-strand	178-179	2	4
β-strand	184-193	10	4
α-helix	194-196	3
β-strand	203-208	6	5
α-helix	209-211	3
β-strand	213-218	6	5

Chain L: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	33-38	6	7
β-strand	45-49	5	7
β-strand	53-54	2	7
α-helix	55	1
β-strand	62-67	6	6
β-strand	70-75	6	6
α-helix	80-82	3
β-strand	85-90	6	7
β-strand	98	1	7
β-strand	102-106	5	7
α-helix	112-113	2
β-strand	114-118	5	8
α-helix	119-121	3
α-helix	122-127	6
β-strand	129-139	11	8
β-strand	145-151	7	9
β-strand	153-154	2	9
β-strand	161-163	3	8
α-helix	164-167	4
β-strand	173-182	10	8
α-helix	183-186	4
β-strand	191-198	8	9
β-strand	201-210	10	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
A10F9 Fab heavy chain	E, H	protein	224	Mus musculus	A0N7J2 (AlphaFold model)
A10F9 Fab light chain	F, L	protein	214	Mus musculus	I6L978 (AlphaFold model)
Gag protein	C, D	protein	231	Human immunodeficiency virus 1	Q9DGV7

Sequence of entity 1 (E, H), FASTA

>3VRL_1 A10F9 Fab heavy chain (chains E, H)
DVKLVESGGGLVKPGGSLKLSCAASGFTFSSYTMSWVRQTPEKRLEWVAIISSGGSYTYY
SDSVKGRFTISRDNAKNTLYLQMSSLKSEDTAMYYCTRDEGNGNYVEAMDYWGQGTSVTV
SSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 2 (F, L), FASTA

>3VRL_2 A10F9 Fab light chain (chains F, L)
DIQMTQSPASLSASVGETVTITCRASGNIHNYLAWYQQKQGKSPQLLVYNAKTLADGVPS
RFSGSGSGTQYSLKINSLQPEDFGSYYCQHFWSTPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 3 (C, D), FASTA

>3VRL_3 Gag protein (chains C, D)
PIVQNLQGQMVHQPISPRTLNAWVKVIEEKGFSPEVIPMFTALSEGATPQDLNTMLNTVG
GHQAAMQMLKDTINEEAAEWDRLHPVQAGPVAPGQMRDPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGDIYKRWIILGLNKIVRMYSPVSILDIKQGPKESFRDYVDRFFKTLRAEQCTQD
VKNWMTDTLLVQNANPDCKTILRALGPGATLEEMMTACQGVGGPSHKARVL

Primary citation

Structure of the HIV-1 capsid protein p24 in complex with the broad-spectrum antibody A10F9. Gu, Y., Cao, F., Li, S. et al. To be published.

Other PDB entries of the same protein (UniProt A0N7J2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2OK0 1.89 Å, Fab ED10-DNA complex
2OJZ 2.73 Å, Anti-DNA antibody ED10

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