4RWY: HIV-1 YU2 gp120

Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131 in complex with HIV-1 clade B YU2 gp120. Determined by X-ray diffraction at 2.13 Å resolution. Released 1 Jul 2015.

Method: X-ray diffraction
Resolution: 2.13 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 6,374
Mol. weight: 91.35 kDa
Ligands: NAG
Released: 1 Jul 2015

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

Secondary structure: helices and β-sheets

4RWY contains 26 α-helices and 69 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 A: 10 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	1
β-strand	53-55	3	2
α-helix	65-73	9
β-strand	74-75	2	2
α-helix	76-78	3
β-strand	83-85	3	1
β-strand	91-94	4	3
α-helix	95-97	3
α-helix	99-115	17
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
α-helix	248-250	3
β-strand	251	1	5
β-strand	259-261	3	6
β-strand	271-273	3	6
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-353	19
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
β-strand	393	1	6
β-strand	413-420	8	6
β-strand	423-424	2	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	486-490	5	1

Chain H: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	7
β-strand	10-12	3	8
β-strand	18-24	7	7
α-helix	26-31	6
β-strand	33-39	7	8
β-strand	46-51	6	8
β-strand	57-59	3	8
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
β-strand	102-103	2	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	125-127	3
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chain L: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-13	4	13
α-helix	18	1
β-strand	19-30	11	12
β-strand	34-38	5	13
β-strand	45-49	5	13
β-strand	53-54	2	13
β-strand	62-75	14	12
α-helix	80-82	3
β-strand	85-89	5	13
α-helix	97	1
β-strand	98	1	13
α-helix	99	1
β-strand	102-106	5	13
β-strand	111	1	14
β-strand	114-118	5	15
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	15
β-strand	140	1	14
β-strand	145-150	6	16
β-strand	153-155	3	16
β-strand	159-163	5	15
α-helix	164-167	4
β-strand	173-182	10	15
α-helix	183-186	4
β-strand	191-197	7	16
β-strand	205-210	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 YU2 gp120	A	protein	376	Human immunodeficiency virus 1	P35961
Antibody 8ANC131 Heavy chain	H	protein	227	Homo sapiens
Antibody 8ANC131 Light chain	L	protein	213	Homo sapiens

Sequence of entity 1 (A), FASTA

>4RWY_1 HIV-1 YU2 gp120 (chains A)
MPMGSLQPLATLYLLGMLVASVLAVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDP
NPQEVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEP
IPIHYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVI
RSENFTNNAKTIIVQLNESVVINCTRPNNGGSGSGGDIRQAHCNLSKTQWENTLEQIAIK
LKEQFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITL
PCRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMR
DNWRSELYKYKVVKIE

Sequence of entity 2 (H), FASTA

>4RWY_2 Antibody 8ANC131 Heavy chain (chains H)
QGQLVQSGGGLKKPGTSVTISCLASEYTFNEFVIHWIRQAPGQGPLWLGLIKRSGRLMTA
YNFQDRLSLRRDRSTGTVFMELRGLRPDDTAVYYCARDGLGEVAPDYRYGIDVWGQGSTV
IVTSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKAEPKSC

Sequence of entity 3 (L), FASTA

>4RWY_3 Antibody 8ANC131 Light chain (chains L)
EIVLTQSPATLSLSPGERATLSCRASQGLNFVVWYQQKRGQAPRLLIHAPSGRAPGVPDR
FSARGSGTEFSLVISSVEPDDFAIYYCQEYSSTPYNFGPGTRVDRKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6

Water and common crystallization additives (EPE, NA, EDO) are not listed.

Primary citation

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Zhou, T., Lynch, R.M., Chen, L. et al. Cell (2015) 161:1280-1292. DOI 10.1016/j.cell.2015.05.007 · PubMed

Other PDB entries of the same protein (UniProt P35961), best resolution first:

4JZZ 1.49 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4JZW 1.78 Å, Crystal structure of CD4-mimetic miniprotein M48U1 in complex with HIV-1 YU2 gp120 in…
4KA2 1.79 Å, Crystal structure of CD4-mimetic miniprotein M48U12 in complex with HIV-1 YU2 gp120
4K0A 2.13 Å, Crystal structure of CD4-mimetic miniprotein M48U7 in complex with HIV-1 YU2 gp120
4LAJ 2.14 Å, Crystal structure of HIV-1 YU2 envelope gp120 glycoprotein in complex with CD4-mimetic…
1YYM 2.2 Å, crystal structure of F23, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2 gp120…
2NY7 2.3 Å, HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing…
2I60 2.4 Å, Crystal structure of [Phe23]M47, a scorpion-toxin mimic of CD4, in complex with HIV-1…
4DVR 2.5 Å, Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557
4JO3 2.6 Å, Crystal structure of rabbit mAb R20 Fab in complex with V3 C-terminus of HIV-1 Consensus…
1YYL 2.75 Å, crystal structure of CD4M33, a scorpion-toxin mimic of CD4, in complex with HIV-1 YU2…
1G9N 2.9 Å, HIV-1 YU2 GP120 envelope glycoprotein complexed with CD4 and induced neutralizing…

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