4XVT: Envelope glycoprotein GP120 of HIV-1 clade a/e

Crystal structure of HIV-1 93TH057 coreE gp120 with antibody 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995). Determined by X-ray diffraction at 1.69 Å resolution. Released 15 Jul 2015.

Method: X-ray diffraction
Resolution: 1.69 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,818
Mol. weight: 89.54 kDa
Ligands: NAG
Released: 15 Jul 2015

Explore 4XVT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4XVT contains 29 α-helices and 72 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 G: 11 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	45-47	3	1
β-strand	53-56	4	2
α-helix	65-73	9
β-strand	74-76	3	2
β-strand	83-86	4	1
β-strand	91-94	4	3
α-helix	99-115	17
β-strand	120-122	3	4
β-strand	200-202	3	4
β-strand	215-218	4	2
α-helix	219-220	2
β-strand	223-228	6	1
β-strand	236-239	4	3
β-strand	242-245	4	1
β-strand	247	1	2
α-helix	248-250	3
β-strand	251	1	2
β-strand	259-261	3	5
β-strand	271-273	3	5
β-strand	284-298	15	5
β-strand	328-334	7	5
α-helix	335-352	18
β-strand	358-361	4	5
α-helix	369-372	4
β-strand	374-378	5	5
β-strand	381-385	5	5
α-helix	388-390	3
α-helix	393-396	4
β-strand	413-421	9	5
β-strand	423-425	3	4
β-strand	432-434	3	4
α-helix	436-439	4
β-strand	443-456	14	5
α-helix	457	1
β-strand	465-470	6	5
α-helix	475-483	9
β-strand	486-491	6	1

Chain H: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-52	8	7
β-strand	57-59	3	7
α-helix	62-64	3
β-strand	68-73	6	6
α-helix	74-76	3
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
β-strand	101-102	2	8
β-strand	107-108	2	8
β-strand	114-115	2	7
β-strand	119-123	5	7
β-strand	129	1	9
α-helix	130-131	2
β-strand	132-136	5	10
α-helix	140-142	3
β-strand	143-144	2	10
β-strand	147-157	11	10
β-strand	158	1	9
β-strand	163-166	4	11
α-helix	167-169	3
β-strand	171	1	11
β-strand	175-177	3	10
α-helix	178-180	3
β-strand	181-182	2	10
β-strand	188-197	10	10
α-helix	198-202	5
β-strand	207-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	12
β-strand	12-14	3	13
β-strand	21-27	7	12
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
α-helix	80-82	3
β-strand	84-90	7	13
β-strand	97-98	2	13
β-strand	102-105	4	13
β-strand	113	1	14
α-helix	114-115	2
β-strand	116-120	5	15
α-helix	121-123	3
α-helix	124-128	5
β-strand	131-141	11	15
β-strand	142	1	14
β-strand	147-152	6	16
β-strand	155-156	2	16
α-helix	157	1
β-strand	161-165	5	15
α-helix	166-169	4
β-strand	175-184	10	15
α-helix	185-188	4
β-strand	193-199	7	16
β-strand	207-212	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein GP120 of HIV-1 clade a/e	G	protein	353	Human immunodeficiency virus 1	Q0ED31
donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain	H	protein	228	Homo sapiens
45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain	L	protein	210	Homo sapiens

Sequence of entity 1 (G), FASTA

>4XVT_1 ENVELOPE GLYCOPROTEIN GP120 OF HIV-1 CLADE A/E (chains G)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (H), FASTA

>4XVT_2 donor 45 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Heavy chain (chains H)
QVQLLQSGAQVKKTGASMRISCKTSGYTFLNCPINWVRQAPGRGLEWMGWMKPRGGAVNY
PQKFQGRVTMTRDMSTDTAFLDMSNLRSDDTAVYFCARGKYCTASDYYNWDFEHWGRGTL
VTVSSPATKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>4XVT_3 45-VRC01.H01+07.O-863513/45-VRC01.L01+07.O-110653 (VRC07_1995) Light chain (chains L)
EIVLTQSPGTLSLSPGERATLSCRTSQYGSLAWYQQRPGQAPRLVIYGGSSRATGIPDRF
TGSRSGADYTLTINRLEPEDFGIYYCQQYEFFGQGTKVEVDIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLASPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

Primary citation

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Wu, X., Zhang, Z., Schramm, C.A. et al. Cell (2015) 161:470-485. DOI 10.1016/j.cell.2015.03.004 · PubMed

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

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…
4OM1 2.13 Å, Crystal structure of antibody VRC07-I30Q, G54W, S58N in complex with clade A/E 93TH057…

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