3NGB: Broadly and potently neutralizing antibody VRC01

Crystal structure of broadly and potently neutralizing antibody VRC01 in complex with HIV-1 gp120. Determined by X-ray diffraction at 2.68 Å resolution. Released 7 Jul 2010.

Method: X-ray diffraction
Resolution: 2.68 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 25,808
Mol. weight: 363.54 kDa
Ligands: NAG, BGC
Released: 7 Jul 2010

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

Secondary structure: helices and β-sheets

3NGB contains 83 α-helices and 319 β-strands across 12 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: 10 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	18
β-strand	53-56	4	19
α-helix	65-69	5
β-strand	75-76	2	19
α-helix	77-78	2
β-strand	84-85	2	18
β-strand	92-94	3	20
α-helix	99-112	14
β-strand	120-123	4	21
β-strand	199-202	4	21
β-strand	215	1	22
β-strand	216-218	3	19
β-strand	223-228	6	18
β-strand	236-238	3	20
β-strand	242-245	4	18
β-strand	247	1	19
β-strand	251	1	22
β-strand	256	1	23
β-strand	259-261	3	24
α-helix	264-266	3
β-strand	271-273	3	24
β-strand	284-298	15	24
β-strand	328-334	7	24
α-helix	335-349	15
β-strand	353	1	25
β-strand	355	1	25
β-strand	358	1	26
β-strand	361	1	24
α-helix	369-372	4
β-strand	374-378	5	23
β-strand	381-385	5	23
α-helix	388-390	3
α-helix	393-396	4
β-strand	413-419	7	24
β-strand	420	1	23
β-strand	423-425	3	21
β-strand	432-434	3	21
α-helix	436-439	4
β-strand	443-456	14	24
β-strand	463	1	26
β-strand	465	1	26
β-strand	468-470	3	24
α-helix	476-483	8
β-strand	486-491	6	18

Chain B: 5 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	27
β-strand	10-12	3	28
β-strand	18-25	8	27
β-strand	34-39	6	28
β-strand	46-51	6	28
β-strand	57-59	3	28
α-helix	61-63	3
β-strand	67-72	6	27
β-strand	77-82	6	27
α-helix	84-86	3
β-strand	88-97	10	28
β-strand	100-103	8	28
β-strand	107-111	5	28
β-strand	117	1	29
α-helix	118-119	2
β-strand	120-124	5	30
β-strand	135-145	11	30
β-strand	146	1	29
β-strand	151-154	4	31
β-strand	159	1	31
β-strand	163-165	3	30
α-helix	166-168	3
β-strand	169-170	2	30
β-strand	176-185	10	30
β-strand	194-200	7	31
α-helix	201-203	3
β-strand	205-211	7	31

Chain C: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	32
β-strand	10-13	4	33
β-strand	15	1	34
β-strand	17	1	34
α-helix	18	1
β-strand	19-24	6	32
β-strand	33-38	6	33
β-strand	45-49	5	33
β-strand	53-54	2	33
β-strand	62-67	6	32
β-strand	70-75	6	32
α-helix	80-82	3
β-strand	84-90	7	33
β-strand	97-98	2	33
β-strand	102-106	5	33
α-helix	111-112	2
β-strand	113	1	35
β-strand	116-117	2	36
β-strand	120	1	37
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-134	4	38
β-strand	135	1	37
β-strand	137-141	5	36
β-strand	142	1	35
β-strand	147-152	6	39
β-strand	155-156	2	39
β-strand	163-165	3	36
β-strand	175-179	5	36
β-strand	181-184	4	38
α-helix	185-188	4
β-strand	193-199	7	39
β-strand	207	1	39
β-strand	210-212	3	39

Chain D: 9 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	40
β-strand	53-56	4	41
α-helix	65-73	9
β-strand	75-76	2	41
β-strand	84-85	2	40
β-strand	91-94	4	42
α-helix	99-113	15
β-strand	120-123	4	43
β-strand	199-202	4	43
β-strand	215	1	44
β-strand	216-218	3	41
β-strand	223-228	6	40
β-strand	236-239	4	42
β-strand	242-245	4	40
β-strand	247	1	41
β-strand	251	1	44
β-strand	256	1	45
β-strand	259-261	3	45
α-helix	264-266	3
β-strand	271-273	3	45
β-strand	284-298	15	45
β-strand	328-334	7	45
α-helix	335-349	15
α-helix	357	1
β-strand	358-361	4	45
α-helix	369-372	4
β-strand	374-378	5	45
β-strand	381-385	5	45
α-helix	393-396	4
β-strand	413-421	9	45
β-strand	423-425	3	43
β-strand	432-434	3	43
α-helix	436-439	4
β-strand	443-456	14	45
β-strand	465-470	6	45
α-helix	476-483	8
β-strand	488-491	4	40

Chain E: 7 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	46
β-strand	10-12	3	47
β-strand	14	1	48
β-strand	16	1	48
β-strand	18-25	8	46
β-strand	34-39	6	47
β-strand	46-52	7	47
β-strand	56-59	4	47
α-helix	61-63	3
β-strand	67-72	6	46
α-helix	73-75	3
β-strand	77-82	6	46
α-helix	84-86	3
β-strand	88-93	6	47
β-strand	94-97	4	49
β-strand	100-102	7	49
β-strand	107-111	5	47
β-strand	117	1	50
β-strand	120	1	51
β-strand	123-124	2	52
β-strand	135	1	53
β-strand	138-140	3	52
β-strand	143	1	51
β-strand	145	1	54
β-strand	146	1	50
β-strand	152-154	3	55
β-strand	163-165	3	52
α-helix	166-168	3
β-strand	176	1	54
β-strand	180-182	3	52
β-strand	185	1	53
α-helix	186-188	3
β-strand	195-198	4	55
α-helix	201-203	3
β-strand	209-210	2	55
α-helix	212-214	3

Chain F: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	56
β-strand	10-13	4	57
β-strand	19-25	7	56
β-strand	34-38	5	57
α-helix	43-44	2
β-strand	45-49	5	57
β-strand	53-54	2	57
α-helix	55	1
β-strand	62-67	6	56
β-strand	70-75	6	56
β-strand	84-90	7	57
β-strand	97-98	2	57
β-strand	102-106	5	57
β-strand	113	1	58
β-strand	117	1	59
β-strand	120	1	59
β-strand	135-138	4	59
β-strand	142	1	58
β-strand	147-152	6	60
β-strand	156	1	60
β-strand	161	1	61
β-strand	177-180	4	59
β-strand	181	1	61
α-helix	185-188	4
β-strand	193	1	62
β-strand	194-199	6	60
β-strand	207	1	60
β-strand	212	1	62

Chain G: 12 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	1
β-strand	53-55	3	2
α-helix	65-73	9
β-strand	75	1	2
α-helix	76-78	3
β-strand	84-85	2	1
β-strand	91-94	4	3
α-helix	95-97	3
α-helix	99-113	15
β-strand	120-122	3	4
β-strand	201-202	2	4
α-helix	212-214	3
β-strand	215	1	5
β-strand	216-218	3	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
β-strand	251	1	5
β-strand	256	1	6
β-strand	259-261	3	6
α-helix	264-266	3
β-strand	271-273	3	6
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-349	15
β-strand	353	1	7
β-strand	355	1	7
β-strand	358-361	4	6
α-helix	369-372	4
β-strand	374-378	5	6
β-strand	381-385	5	6
α-helix	388-391	4
α-helix	394-397	4
β-strand	413-420	8	6
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	6
β-strand	465-470	6	6
α-helix	476-483	8
β-strand	488-491	4	1

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
β-strand	10-12	3	9
β-strand	18-25	8	8
β-strand	34-39	6	9
β-strand	46-52	7	9
β-strand	56-59	4	9
α-helix	61-63	3
β-strand	67-72	6	8
β-strand	77-82	6	8
α-helix	84-86	3
β-strand	88-95	8	9
β-strand	100D-103	4	9
β-strand	104	1	8
β-strand	107-111	5	9
β-strand	117	1	10
β-strand	120-121	2	11
β-strand	124	1	11
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	12
β-strand	159	1	12
β-strand	164-165	2	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-189	4
β-strand	195-200	6	12
α-helix	201-203	3
β-strand	205-210	6	12

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	A, D, G, I	protein	353	Human immunodeficiency virus 1	Q0ED31
Antigen binding fragment of heavy chain: Antibody VRC01	B, E, H, J	protein	224	Homo sapiens
Antigen binding fragment of light chain: Antibody VRC01	C, F, K, L	protein	210	Homo sapiens

Sequence of entity 1 (A, D, G, I), FASTA

>3NGB_1 Envelope glycoprotein gp160 (chains A, D, G, I)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (B, E, H, J), FASTA

>3NGB_2 Antigen binding fragment of heavy chain: Antibody VRC01 (chains B, E, H, J)
QVQLVQSGGQMKKPGESMRISCRASGYEFIDCTLNWIRLAPGKRPEWMGWLKPRGGAVNY
ARPLQGRVTMTRDVYSDTAFLELRSLTVDDTAVYFCTRGKNCDYNWDFEHWGRGTPVIVS
SPSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQS
SGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC

Sequence of entity 3 (C, F, K, L), FASTA

>3NGB_3 Antigen binding fragment of light chain: Antibody VRC01 (chains C, F, K, L)
EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRF
SGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	46
BGC	beta-D-glucopyranose	C6 H12 O6	13

Water and common crystallization additives (TRS) are not listed.

Primary citation

Structural basis for broad and potent neutralization of HIV-1 by antibody VRC01. Zhou, T., Georgiev, I., Wu, X. et al. Science (2010) 329:811-817. DOI 10.1126/science.1192819 · PubMed

Other PDB entries of the same protein (UniProt Q0ED31), best resolution first:

4XVT 1.69 Å, Crystal structure of HIV-1 93TH057 coreE gp120 with antibody…
4DKP 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-50
4DKR 1.8 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with AWS-I-169
4YDL 1.8 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC18.02 in complex…
4H8W 1.85 Å, Crystal structure of non-neutralizing and ADCC-potent antibody N5-i5 in complex with…
4DKQ 1.89 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with DMJ-I-228
3SE8 1.9 Å, Crystal structure of broadly and potently neutralizing antibody VRC03 in complex with…
3TGT 1.9 Å, Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core
4DKO 1.98 Å, Crystal structure of clade A/E 93TH057 HIV-1 gp120 core in complex with TS-II-224
3SE9 2.0 Å, Crystal structure of broadly and potently neutralizing antibody VRC-PG04 in complex with…
4YDK 2.05 Å, Crystal structure of broadly and potently neutralizing antibody C38-VRC16.01 in complex…
4OLZ 2.1 Å, Crystal structure of antibody VRC07-G54W in complex with clade A/E 93TH057 HIV-1 gp120…

Browse more

3NGB is part of these collections:

Antibodies and the immune system

About this viewer

MolViewer shows 3NGB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.