4DVR: YU2 gp120 core

Crystal structure of YU2 gp120 core in complex with Fab 48d and NBD-557. Determined by X-ray diffraction at 2.5 Å resolution. Released 27 Feb 2013.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Human immunodeficiency virus type 1 group M subtype B (isolate YU-2), Homo sapiens
Chains: 3
Atoms: 5,767
Mol. weight: 83.33 kDa
Ligands: 0LY, NAG
Released: 27 Feb 2013

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

Secondary structure: helices and β-sheets

4DVR contains 20 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 G: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	92-94	3	1
α-helix	100-115	16
β-strand	120-122	3	2
β-strand	200-202	3	2
β-strand	215	1	3
β-strand	218	1	4
β-strand	223-228	6	5
β-strand	236-238	3	1
β-strand	242-245	4	5
β-strand	247	1	4
β-strand	251	1	3
β-strand	256	1	6
β-strand	259-261	3	6
α-helix	264-266	3
β-strand	271-274	4	6
α-helix	283	1
β-strand	284-298	15	6
β-strand	328-334	7	6
α-helix	335-353	19
β-strand	359-361	3	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	413-421	9	6
β-strand	423-425	3	2
β-strand	432-434	3	2
α-helix	435-439	5
β-strand	443-456	14	6
β-strand	466-470	5	6
α-helix	475-480	6
β-strand	486-490	5	5

Chain H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	12
α-helix	7-9	3
β-strand	10-12	3	13
β-strand	18-25	8	12
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-52	8	13
β-strand	57-60	4	13
β-strand	68-73	6	12
β-strand	78-83	6	12
α-helix	88-90	3
β-strand	92-98	7	13
β-strand	108-109	2	13
β-strand	113-117	5	13
α-helix	121-122	2
β-strand	123	1	14
β-strand	126-130	5	15
β-strand	137-138	2	15
β-strand	141-151	11	15
β-strand	152	1	14
β-strand	157-160	4	16
β-strand	165	1	16
β-strand	169-171	3	15
α-helix	172-174	3
β-strand	175-176	2	15
β-strand	182-191	10	15
α-helix	192-194	3
β-strand	200-206	7	16
α-helix	207-209	3
β-strand	211-217	7	16

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	33-38	6	8
α-helix	43-44	2
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-67	6	7
β-strand	70-75	6	7
β-strand	85-90	6	8
β-strand	97	1	8
β-strand	101-105	5	8
β-strand	110	1	9
β-strand	113-117	5	10
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	10
β-strand	139	1	9
β-strand	144-149	6	11
β-strand	152-154	3	11
β-strand	158-162	5	10
α-helix	163-166	4
β-strand	172-181	10	10
α-helix	182-186	5
β-strand	190-196	7	11
β-strand	204-209	6	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp120	G	protein	313	Human immunodeficiency virus type 1 group M subtype B (isolate YU-2)	P35961
Fab 48d Light chain	L	protein	212	Homo sapiens
Fab 48d Heavy chain	H	protein	219	Homo sapiens

Sequence of entity 1 (G), FASTA

>4DVR_1 Envelope glycoprotein gp120 (chains G)
EVKLENVTENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTGGSVITQACPKVSFEPIPI
HYCAPAGFAILKCNDKKFNGTGPCTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSE
NFTNNAKTIIVQLNESVVINCTRPNNGGSGSGGDIRQAHCNLSKTQWENTLEQIAIKLKE
QFGNNKTIIFNPSSGGDPEIVTHSFNCGGEFFYCNSTQLFTWNDTRKLNNTGRNITLPCR
IKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGKDTNGTEIFRPGGGDMRDNW
RSELYKYKVVKIE

Sequence of entity 2 (L), FASTA

>4DVR_2 Fab 48d Light chain (chains L)
DIQMTQSPSSVSASVGDRVTITCRASQDISTWLAWYQQKPGKAPKLLIYAASTLQSGVPS
RFSGSGSGTDFSLTINSLQPEDFATYYCQQANSFFTFGGGTKVEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKLYACEVTHQGLSSPVTKSFNRGE

Sequence of entity 3 (H), FASTA

>4DVR_3 Fab 48d Heavy chain (chains H)
EVQLVQSGAEVKKPGATVKISCKASGYTFSDFYMYWVRQAPGKGLEWMGLIDPEDADTMY
AEKFRGRVTITADTSTDTGYLELSSLRSEDTAVYYCAADPWELNAFNVWGQGTLVSVSSA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Ligands and cofactors

ID	Name	Formula	Copies
0LY	N-(4-bromophenyl)-N'-(2,2,6,6-tetramethylpiperidin-4-yl)ethanediamide	C17 H24 Br N3 O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Crystal Structures of HIV-1 gp120 Envelope Glycoprotein in Complex with NBD Analogues That Target the CD4-Binding Site. Kwon, Y.D., Lalonde, J.M., Yang, Y. et al. PLoS One (2014) 9:e85940-e85940. DOI 10.1371/journal.pone.0085940 · 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
4RWY 2.13 Å, Crystal structure of VH1-46 germline-derived CD4-binding site-directed antibody 8ANC131…
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…
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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