1GC1: HIV-1 GP120 core

HIV-1 GP120 core complexed with CD4 and a neutralizing human antibody. Determined by X-ray diffraction at 2.5 Å resolution. Released 8 Jul 1998.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 4
Atoms: 7,877
Mol. weight: 106.8 kDa
Ligands: NAG
Released: 8 Jul 1998

Explore 1GC1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1GC1 contains 24 α-helices and 91 β-strands across 4 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: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	2-7	6	9
β-strand	12-14	3	10
β-strand	17	1	11
β-strand	27-29	3	9
β-strand	35-40	6	9
β-strand	43-46	4	9
β-strand	55-56	2	10
α-helix	59-64	6
β-strand	66	1	11
β-strand	69-71	3	10
α-helix	76-78	3
β-strand	80-85	6	9
β-strand	90-98	9	9
β-strand	99-102	4	12
β-strand	107-109	3	13
β-strand	114-119	6	12
β-strand	127-131	5	14
β-strand	137-140	4	14
β-strand	143-146	4	12
α-helix	151-153	3
β-strand	155-163	9	14
β-strand	166-174	9	14
β-strand	175-177	3	13

Chain G: 10 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	92-94	3	1
α-helix	101-115	15
β-strand	120-122	3	2
α-helix	124-126	3
β-strand	128	1	3
β-strand	195	1	3
β-strand	199-200	2	2
α-helix	212-214	3
β-strand	215	1	4
α-helix	216	1
β-strand	218	1	5
β-strand	223-228	6	6
β-strand	237-239	3	1
β-strand	242-245	4	6
β-strand	247	1	5
β-strand	251	1	4
β-strand	256	1	7
β-strand	261	1	8
α-helix	264-266	3
β-strand	271-273	3	8
β-strand	284-297	14	8
β-strand	330-334	5	8
α-helix	335-346	12
α-helix	349-353	5
β-strand	358-361	4	8
β-strand	367	1	9
α-helix	369-372	4
β-strand	374-378	5	7
β-strand	381-385	5	7
β-strand	393-395	3	8
β-strand	413-417	5	8
β-strand	418-420	3	7
β-strand	423-425	3	2
β-strand	431-434	4	2
α-helix	436-438	3
β-strand	444-456	13	8
β-strand	465-470	6	8
α-helix	476-483	8
β-strand	488-490	3	6

Chain H: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	21
β-strand	10-12	3	22
β-strand	18-25	8	21
α-helix	29-31	3
β-strand	32-39	8	22
β-strand	45-52	8	22
β-strand	57-60	4	22
β-strand	68-73	6	21
β-strand	78-83	6	21
α-helix	88-90	3
β-strand	92-100	9	22
β-strand	117-118	2	22
β-strand	122-126	5	22
α-helix	130-131	2
β-strand	135-139	5	23
β-strand	150-160	11	23
β-strand	165-169	5	24
α-helix	170-172	3
β-strand	174	1	24
β-strand	178-180	3	23
α-helix	181-183	3
β-strand	184-185	2	23
β-strand	191-200	10	23
β-strand	210-215	6	24
β-strand	220-225	6	24

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
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	62-67	6	15
β-strand	70-75	6	15
β-strand	84-90	7	16
β-strand	99-100	2	16
β-strand	104-108	5	16
β-strand	116-120	5	17
α-helix	121-123	3
α-helix	124-129	6
β-strand	131-141	11	17
β-strand	147-150	4	18
β-strand	151	1	19
β-strand	156	1	19
β-strand	161-165	5	17
α-helix	166-169	4
β-strand	175-184	10	17
α-helix	185-188	4
β-strand	189	1	20
β-strand	191	1	20
β-strand	193-199	7	18
β-strand	207-212	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope protein GP120	G	protein	321	Human immunodeficiency virus 1	P04578 (AlphaFold model)
CD4	C	protein	185	Homo sapiens	P01730 (AlphaFold model)
Antibody 17B	L	protein	213	Homo sapiens
Antibody 17B	H	protein	229	Homo sapiens

Sequence of entity 1 (G), FASTA

>1GC1_1 ENVELOPE PROTEIN GP120 (chains G)
GARSEVVLVNVTENFNMWKNDMVEQMHEDIISLWDQSLKPCVKLTPLCVGAGSCNTSVIT
QACPKVSFEPIPIHYCAPAGFAILKCNNKTFNGTGPCTNVSTVQCTHGIRPVVSTQLLLN
GSLAEEEVVIRSVNFTDNAKTIIVQLNTSVEINCTGAGHCNISRAKWNNTLKQIASKLRE
QFGNNKTIIFKQSSGGDPEIVTHSFNCGGEFFYCNSTQLFNSTWFNSTWSTKGSNNTEGS
DTITLPCRIKQIINMWQKVGKAMYAPPISGQIRCSSNITGLLLTRDGGNSNNESEIFRPG
GGDMRDNWRSELYKYKVVKIE

Sequence of entity 2 (C), FASTA

>1GC1_2 CD4 (chains C)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KASNT

Sequence of entity 3 (L), FASTA

>1GC1_3 ANTIBODY 17B (chains L)
ELELTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 4 (H), FASTA

>1GC1_4 ANTIBODY 17B (chains H)
QVQLLESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPQPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Kwong, P.D., Wyatt, R., Robinson, J. et al. Nature (1998) 393:648-659. DOI 10.1038/31405 · PubMed

Other PDB entries of the same protein (UniProt P04578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8F3A 1.2 Å, HIV-1 gp41 coiled-coil pocket IQN17
6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
9ARN 1.41 Å, Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal…
1DF4 1.45 Å, Interactions between HIV-1 GP41 core and detergents and their implications for membrane…
6BXP 1.45 Å, Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
7EKB 1.45 Å, Crystal structure of 4E10 modified with pyrene acetamide
5X08 1.49 Å, Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with…
6JQK 1.5 Å, Structure of C34M/N36
5TKK 1.55 Å, Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex…
6PDR 1.55 Å, Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion…

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1GC1 is part of these collections:

Viruses

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