4OM1: Antibody VRC07-I30Q, G54W, S58N

Crystal structure of antibody VRC07-I30Q, G54W, S58N in complex with clade A/E 93TH057 HIV-1 gp120 core. Determined by X-ray diffraction at 2.13 Å resolution. Released 3 Sept 2014.

Method: X-ray diffraction
Resolution: 2.13 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,482
Mol. weight: 89.62 kDa
Ligands: NAG
Released: 3 Sept 2014

Explore 4OM1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4OM1 contains 28 α-helices and 75 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, 28 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
α-helix	77-78	2
β-strand	84-86	3	1
β-strand	91-94	4	3
α-helix	95-97	3
α-helix	100-113	14
β-strand	120-123	4	4
β-strand	199-202	4	4
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	335-352	18
α-helix	357	1
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
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	486-491	6	1

Chain H: 10 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7-9	3
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	46-52	7	8
β-strand	56-59	4	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-94	7	8
β-strand	97-98	2	9
β-strand	100C-100D	2	9
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	117	1	10
α-helix	118-119	2
β-strand	120-124	5	11
β-strand	132	1	12
β-strand	134	1	12
β-strand	135-145	11	11
β-strand	146	1	10
β-strand	151-154	4	13
α-helix	155-157	3
β-strand	159	1	13
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-185	10	11
α-helix	186-188	3
β-strand	195-200	6	13
α-helix	201-203	3
β-strand	205-210	6	13
α-helix	213-215	3

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	14
β-strand	10-13	4	15
β-strand	19-25	7	14
β-strand	33-38	6	15
β-strand	45-49	5	15
β-strand	53-54	2	15
α-helix	55	1
β-strand	62-67	6	14
β-strand	70-75	6	14
α-helix	80-82	3
β-strand	84-90	7	15
β-strand	97-98	2	15
β-strand	102-106	5	15
β-strand	113	1	16
α-helix	114-115	2
β-strand	116-120	5	17
α-helix	121-123	3
α-helix	124-127	4
β-strand	131-141	11	17
β-strand	142	1	16
β-strand	147-152	6	18
β-strand	155-156	2	18
β-strand	161-165	5	17
α-helix	166-169	4
β-strand	175-184	10	17
α-helix	185-188	4
β-strand	193-199	7	18
β-strand	207-212	6	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	G	protein	353	Human immunodeficiency virus 1	Q0ED31
Antigen binding fragment of heavy chain: Antibody VRC01	H	protein	228	Homo sapiens
Antigen binding fragment of light chain: Antibody VRC01	L	protein	210	Homo sapiens

Sequence of entity 1 (G), FASTA

>4OM1_1 Envelope glycoprotein gp160 (chains G)
VWKDADTTLFCASDAKAHETEVHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQ
MQEDVISLWDQSLQPCVKLTGGSVIKQACPKISFDPIPIHYCTPAGYVILKCNDKNFNGT
GPCKNVSSVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNKSVEINC
TRPSNGGSGSGGDIRKAYCEINGTKWNKVLKQVTEKLKEHFNNKTIIFQPPSGGDLEITM
HHFNCRGEFFYCNTTQLFNNTCIGNETMKGCNGTITLPCKIKQIINMWQGTGQAMYAPPI
DGKINCVSNITGILLTRDGGANNTSNETFRPGGGNIKDNWRSELYKYKVVQIE

Sequence of entity 2 (H), FASTA

>4OM1_2 Antigen binding fragment of heavy chain: Antibody VRC01 (chains H)
QVRLSQSGGQMKKPGDSMRISCRASGYEFQNCPINWIRLAPGKRPEWMGWMKPRWGAVNY
ARQLQGRVTMTRDMYSETAFLELRSLTSDDTAVYFCTRGKYCTARDYYNWDFEHWGQGTP
VTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 3 (L), FASTA

>4OM1_3 Antigen binding fragment of light chain: Antibody VRC01 (chains L)
EIVLTQSPGTLSLSPGETAIISCRTSQYGSLAWYQQRPGQAPRLVIYSGSTRAAGIPDRF
SGSRWGPDYNLTISNLESGDFGVYYCQQYEFFGQGTKVQVDIKRTVAAPSVFIFPPSDEQ
LKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKA
DYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	10

Primary citation

Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo. Rudicell, R.S., Kwon, Y.D., Ko, S.Y. et al. J Virol (2014) 88:12669-12682. DOI 10.1128/JVI.02213-14 · 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…

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