1E6J: HIV-1 capsid protein

Crystal structure of HIV-1 capsid protein (p24) in complex with Fab13B5. Determined by X-ray diffraction at 3.0 Å resolution. Released 27 Nov 2000.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: MUS MUSCULUS, HIV-1 M\:B_HXB2R
Chains: 3
Atoms: 4,914
Mol. weight: 70.03 kDa
Released: 27 Nov 2000

Explore 1E6J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1E6J contains 33 α-helices and 42 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 H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	17-25	9	1
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	43-51	9	2
β-strand	58-60	3	2
α-helix	62-64	3
β-strand	68-73	6	1
α-helix	74-76	3
β-strand	78-84	7	1
α-helix	88-90	3
β-strand	92-101	10	2
β-strand	105-110	6	2
β-strand	114-118	5	2
α-helix	121-123	3
β-strand	124	1	3
β-strand	127-131	5	4
α-helix	133-134	2
β-strand	142-152	11	4
β-strand	153	1	3
β-strand	158-161	4	5
β-strand	166	1	5
β-strand	170-172	3	4
α-helix	173-175	3
β-strand	176-177	2	4
β-strand	182-191	10	4
α-helix	192-194	3
β-strand	201-206	6	5
α-helix	207-209	3
β-strand	211-216	6	5

Chain L: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	6
β-strand	10-13	4	7
α-helix	17-18	2
β-strand	19-29	11	6
β-strand	32-37	6	7
β-strand	44-48	5	7
β-strand	52-53	2	7
β-strand	61-74	14	6
α-helix	79-81	3
β-strand	83-89	7	7
α-helix	95	1
β-strand	96	1	7
α-helix	97	1
β-strand	100-104	5	7
β-strand	109	1	8
β-strand	112-116	5	9
α-helix	117-119	3
α-helix	120-124	5
β-strand	127-137	11	9
β-strand	138	1	8
β-strand	142-148	7	10
β-strand	151-152	2	10
β-strand	157-161	5	9
α-helix	162-165	4
β-strand	171-180	10	9
α-helix	181-185	5
β-strand	189-196	8	10
β-strand	199-208	10	10

Chain P: 16 helices, 0 β-strands

Element	Residues	Length
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	97-100	4
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-145	20
α-helix	150-152	3
α-helix	161-173	13
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
Immunoglobulin	H	protein	219	MUS MUSCULUS	P01868 (AlphaFold model)
Immunoglobulin	L	protein	210	MUS MUSCULUS	P01837 (AlphaFold model)
Capsid protein P24	P	protein	210	HIV-1 M\:B_HXB2R	P04585 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>1E6J_1 IMMUNOGLOBULIN (chains H)
EVQLQQSGAELARPGASVKMSCKASGYTFTSYTMHWVKQRPGQGLEWIGYINPSSGYSNY
NQKFKDKATLTADKSSSTAYMQLSSLTSEDSAVYYCSRPVVRLGYNFDYWGQGSTLTVSS
AKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSD
LYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVP

Sequence of entity 2 (L), FASTA

>1E6J_2 IMMUNOGLOBULIN (chains L)
EIVLTQSPAITAASLGQKVTITCSASSSVSYMHWYQQKSGTSPKPWIYEISKLASGVPAR
FSGSGSGTSYSLTISSMEAEDAAIYYCQQWNYPFTFGSGTKLEIKRADAAPTVSIFPPSS
EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLT
KDEYERHNSYTCEATHKTSTSPIVKSFNRN

Sequence of entity 3 (P), FASTA

>1E6J_3 CAPSID PROTEIN P24 (chains P)
VHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLK
ETINEEAAEWDRVHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTNNPPIPVGEIY
KRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLL
VQNANPDCKTILKALGPAATLEEMMTACQG

Primary citation

Mutual Conformational Adaptations in Antigen and Antibody Upon Complex Formation between an Fab and HIV-1 Capsid Protein P24. Monaco-Malbet, S., Berthet-Colominas, C., Novelli, A. et al. Structure (2000) 8:1069. DOI 10.1016/S0969-2126(00)00507-4 · PubMed

Other PDB entries of the same protein (UniProt P01868 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1P7K 1.75 Å, Crystal structure of an anti-ssDNA antigen-binding fragment (Fab) bound to…
1SEQ 1.78 Å, Fab MNAC13
1KEL 1.9 Å, Catalytic antibody 28B4 FAB fragment complexed with hapten…
1R3J 1.9 Å, potassium channel KcsA-Fab complex in high concentration of Tl+
2FD6 1.9 Å, Structure of Human Urokinase Plasminogen Activator in Complex with Urokinase Receptor…
5VJQ 1.9 Å, Complex between HyHEL10 Fab fragment heavy chain mutant (I29F, S52T, Y53F) and Pekin…
1GPO 1.95 Å, Crystal structure of the rationally designed antibody M41 as a FAB fragment
3ZO0 1.99 Å, Mouse IgG2a in complex with mouse TRIM21 PRYSPRY
1BM3 2.0 Å, Immunoglobulin OPG2 FAB-peptide complex
1FNS 2.0 Å, Crystal structure of the von willebrand factor (VWF) A1 domain I546V mutant in complex…
1OPG 2.0 Å, OPG2 FAB fragment
1P2C 2.0 Å, crystal structure analysis of an anti-lysozyme antibody

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