4TVP: Envelope glycoprotein gp160

Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising Atomic-Level Definition of Pre-Fusion gp120 and gp41, in Complex with Human Antibodies PGT122 and 35O22. Determined by X-ray diffraction at 3.1 Å resolution. Released 8 Oct 2014.

Method: X-ray diffraction
Resolution: 3.1 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 12,188
Mol. weight: 181.42 kDa
Ligands: NAG
Released: 8 Oct 2014

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

Secondary structure: helices and β-sheets

4TVP contains 49 α-helices and 136 β-strands across 6 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 B: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	524-526	3
β-strand	529	1	11
α-helix	530-533	4
α-helix	537-540	4
α-helix	542-544	3
α-helix	573-595	23
β-strand	603-609	7	1
α-helix	619-622	4
β-strand	627	1	11
α-helix	628-635	8
α-helix	639-647	9
α-helix	654-661	8

Chain D: 9 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	25
α-helix	7-9	3
β-strand	10-12	3	26
β-strand	14	1	27
β-strand	16	1	27
β-strand	18-20	3	28
β-strand	22-27	6	25
α-helix	29-31	3
β-strand	34-40	7	26
β-strand	44-51	8	26
β-strand	57-59	3	26
α-helix	61-63	3
β-strand	67-71	5	28
α-helix	72-72B	3
β-strand	72C-72D	2	25
β-strand	74-77	4	25
β-strand	78-82	5	28
α-helix	84-86	3
β-strand	88-94	7	26
β-strand	102-103	2	26
β-strand	107-111	5	26
α-helix	115-116	2
β-strand	117	1	29
β-strand	120-130	11	30
β-strand	135-145	11	30
β-strand	146	1	29
β-strand	151-154	4	31
β-strand	163-166	4	30
α-helix	167-168	2
β-strand	176-185	10	30
β-strand	195-200	6	31
α-helix	201-203	3
β-strand	205-210	6	31
α-helix	218-221	4

Chain E: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	32
β-strand	5-6	2	33
β-strand	9-14	5	34
β-strand	20-24	5	33
β-strand	32-37	6	34
β-strand	45-49	5	34
β-strand	53-54	2	34
α-helix	55	1
β-strand	62-66	5	33
β-strand	70-75	6	33
α-helix	80-82	3
β-strand	85-91	7	34
β-strand	97-98	2	34
β-strand	99	1	32
β-strand	102-106A	6	34
α-helix	108-110	3
β-strand	111	1	35
β-strand	114-118	5	36
α-helix	119-121	3
β-strand	130-139	10	36
β-strand	140	1	35
β-strand	145-150	6	37
β-strand	154	1	37
β-strand	159-161	3	36
α-helix	162-164	3
β-strand	165-166	2	36
β-strand	172-180	9	36
α-helix	182-185	4
β-strand	191-197	7	37
β-strand	200-206	7	37

Chain G: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	2
β-strand	53	1	3
α-helix	61-63	3
α-helix	74-78	5
β-strand	84-85	2	2
β-strand	91-94	4	4
α-helix	99-114	16
α-helix	120	1
β-strand	121	1	5
α-helix	123-125	3
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	154-160	7	6
β-strand	171-177	7	6
β-strand	181-183	3	6
β-strand	190-193	4	6
β-strand	200-203	4	5
α-helix	204-205	2
β-strand	215	1	7
β-strand	218	1	3
β-strand	223-228	6	2
β-strand	236-239	4	4
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	7
β-strand	259-261	3	8
α-helix	264-266	3
α-helix	270	1
β-strand	271-274	4	8
β-strand	284-298	15	8
β-strand	301	1	9
β-strand	304-307	4	10
β-strand	317-320	4	10
β-strand	323	1	9
β-strand	329-334	6	8
α-helix	335-349	15
β-strand	358-361	4	8
α-helix	369-372	4
β-strand	373-378	6	8
β-strand	381-386	6	8
β-strand	393-395	3	8
β-strand	413-421	9	8
β-strand	423-424	2	5
β-strand	432-435	4	5
α-helix	436-438	3
β-strand	443-456	14	8
β-strand	465-470	6	8
α-helix	476-480	5
β-strand	486-491	6	2
β-strand	494-499	6	1

Chain H: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	20
β-strand	11-12	2	21
β-strand	17-25	9	20
β-strand	33-39	7	16
β-strand	46-51	6	16
β-strand	57-59	3	16
α-helix	61-63	3
β-strand	67-72	6	20
β-strand	77-82A	7	20
α-helix	84-86	3
β-strand	88-100A	14	16
β-strand	100J-100P	7	16
β-strand	105-107	3	16
β-strand	108-109	2	21
α-helix	113-114	2
β-strand	115	1	22
β-strand	118-122	5	23
β-strand	133-143	11	23
β-strand	144	1	22
β-strand	149-152	4	24
α-helix	153-155	3
β-strand	161-164	4	23
α-helix	165-166	2
β-strand	174-183	10	23
β-strand	193-198	6	24
α-helix	199-201	3
β-strand	203-208	6	24

Chain L: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	8-13	5	12
β-strand	18-26	9	13
β-strand	31	1	14
β-strand	34-38	5	12
β-strand	45-48	4	12
β-strand	49	1	15
β-strand	53	1	15
β-strand	62-64	3	13
β-strand	70-76	7	13
α-helix	80-82	3
β-strand	85-89	5	12
β-strand	92	1	14
β-strand	97	1	16
α-helix	98-101	4
β-strand	102-106	5	12
β-strand	112	1	17
β-strand	115-119	5	18
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-138	8	18
β-strand	141	1	17
β-strand	145-151	7	19
β-strand	154-155	2	19
α-helix	156	1
β-strand	160-162	3	18
α-helix	163-165	3
β-strand	166-167	2	18
β-strand	173-181	9	18
α-helix	183-186	4
β-strand	192-198	7	19
β-strand	201-207	7	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	G	protein	481	Human immunodeficiency virus 1	Q2N0S5
Envelope glycoprotein gp160	B	protein	153	Human immunodeficiency virus 1	Q2N0S5
PGT122 Light chain	L	protein	213	Homo sapiens
PGT122 Heavy chain	H	protein	235	Homo sapiens
35O22 Heavy chain	D	protein	243	Homo sapiens
35O22 Light chain	E	protein	216	Homo sapiens

Sequence of entity 1 (G), FASTA

>4TVP_1 Envelope glycoprotein gp160 (chains G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 2 (B), FASTA

>4TVP_2 Envelope glycoprotein gp160 (chains B)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (L), FASTA

>4TVP_3 PGT122 Light chain (chains L)
APTFVSVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSP
GSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVLSQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (H), FASTA

>4TVP_4 PGT122 Heavy chain (chains H)
QVHLQESGPGLVKPSETLSLTCNVSGTLVRDNYWSWIRQPLGKQPEWIGYVHDSGDTNYN
PSLKSRVHLSLDKSKNLVSLRLTGVTAADSAIYYCATTKHGRRIYGVVAFKEWFTYFYMD
VWGKGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 5 (D), FASTA

>4TVP_5 35O22 Heavy chain (chains D)
QGQLVQSGAELKKPGASVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVIMTTDTEVPVTSFTSTGAAYMEIRNLKFDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGLEV
LFQ

Sequence of entity 6 (E), FASTA

>4TVP_6 35O22 Light chain (chains E)
QSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPGI
SPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQSKANPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure and immune recognition of trimeric pre-fusion HIV-1 Env. Pancera, M., Zhou, T., Druz, A. et al. Nature (2014) 514:455-461. DOI 10.1038/nature13808 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S5), best resolution first:

6CDO 2.1 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP16.02 in complex with HIV-1…
6CDM 2.41 Å, Structure of vaccine-elicited HIV-1 neutralizing antibody vFP7.04 in complex with HIV-1…
6CDP 2.46 Å, Vaccine-elicited HIV-1 neutralizing antibody vFP20.01 in complex with HIV-1 fusion…
9P6E 2.7 Å, N49P7-FR Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
9P6G 2.7 Å, eN49P7-FRv1-23 Fab in complex with BG505 MD39 SOSIP and RM20A3 Fab
8TTW 2.96 Å, Cryo-EM structure of BG505 SOSIP.664 HIV-1 Env trimer in complex with temsavir, 8ANC195,…
9Y9V 2.98 Å, The cryoem structure of rhesus macaque 1A8 and PGT121 fabs in complex with BG505…
9Q0W 3.0 Å, Cryo-EM Structure of HIV-1 BG505DS-SOSIP.664 Env Trimer Bound to DFPH-a.01_10R59P_LC Fab
9Q3S 3.01 Å, Cryo-EM structure of PGT121 Fab and Rhesus macaque Ab4 Fab in complex with HIV-1 Env…
5U7M 3.02 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
5U7O 3.03 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
8TKC 3.1 Å, cryo-EM structure of HIV-1 BG505DS-SOSIP.664 env trimer bound to DJ85-b.01 FAB

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4TVP is part of these collections:

Viruses

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