5U7O: HIV-1 BG505 SOSIP.664 Prefusion Env Trimer

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule HIV-1 Entry Inhibitor BMS-626529 in Complex with Human Antibodies PGT122 and 35O22 at 3.8 Angstrom. Determined by X-ray diffraction at 3.03 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 3.03 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 12,066
Mol. weight: 181.41 kDa
Ligands: 83J, NAG
Released: 30 Aug 2017

Explore 5U7O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5U7O contains 41 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: 7 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	529	1	1
α-helix	530-533	4
α-helix	534-536	3
α-helix	539-542	4
α-helix	570-595	26
β-strand	603-609	7	2
α-helix	619-622	4
β-strand	627	1	1
α-helix	628-634	7
α-helix	639-662	24

Chain D: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	10-12	3	4
β-strand	18-25	8	3
α-helix	29-31	3
β-strand	34-40	7	4
β-strand	44-51	8	4
β-strand	57-59	3	4
α-helix	61-63	3
β-strand	67-71	5	3
β-strand	72C-72D	2	5
β-strand	74-75	2	5
β-strand	77-82	6	3
α-helix	84-86	3
β-strand	88-95	8	4
β-strand	100F-103	4	4
β-strand	107-111	5	4
α-helix	115-116	2
β-strand	120-130	11	6
β-strand	135-143	9	6
β-strand	145	1	7
β-strand	151-154	4	8
β-strand	163-166	4	6
α-helix	167	1
β-strand	176	1	7
β-strand	179-182	4	6
β-strand	185	1	6
β-strand	195-200	6	8
β-strand	205-210	6	8

Chain E: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	9
β-strand	5-6	2	10
β-strand	9-14	5	11
β-strand	20-24	5	10
β-strand	32-37	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
α-helix	55	1
β-strand	62-66	5	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	85-91	7	11
β-strand	97-98	2	11
β-strand	99	1	9
β-strand	102-106A	6	11
β-strand	111	1	12
β-strand	114-118	5	13
α-helix	119-121	3
α-helix	122-125	4
β-strand	130-139	10	13
β-strand	140	1	12
β-strand	145-150	6	14
β-strand	154	1	14
β-strand	159-161	3	13
β-strand	165-166	2	13
β-strand	172-180	9	13
α-helix	182-185	4
β-strand	191-197	7	14
β-strand	200-206	7	14

Chain G: 13 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-47	3	15
β-strand	53	1	16
α-helix	75-78	4
β-strand	83-86	4	15
β-strand	91-94	4	17
α-helix	99-115	17
α-helix	120	1
β-strand	121	1	18
β-strand	129	1	19
β-strand	130	1	20
β-strand	133	1	20
β-strand	155-160	6	20
β-strand	171-176	6	20
α-helix	178-180	3
β-strand	181-183	3	19
β-strand	191-193	3	19
α-helix	194-197	4
β-strand	200-203	4	18
α-helix	204-205	2
β-strand	215	1	21
β-strand	218	1	16
β-strand	223-228	6	15
β-strand	236-239	4	17
β-strand	242-245	4	15
β-strand	247	1	16
β-strand	251	1	21
β-strand	259-261	3	22
α-helix	264-266	3
α-helix	270	1
β-strand	271-274	4	22
β-strand	284-298	15	22
β-strand	301	1	23
β-strand	304-308	5	24
β-strand	316-320	5	24
α-helix	321A-322	2
β-strand	323	1	23
β-strand	330-334	5	22
α-helix	335-349	15
β-strand	358-361	4	22
α-helix	369-372	4
β-strand	373-379	7	25
β-strand	381-386	6	25
β-strand	393-395	3	22
β-strand	413-417	5	22
β-strand	418-421	4	25
β-strand	423-425	3	18
β-strand	432-435	4	18
α-helix	436-440	5
β-strand	443-456	14	22
β-strand	465-470	6	22
α-helix	476-480	5
β-strand	488-491	4	15
β-strand	494-499	6	2

Chain H: 5 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	26
β-strand	11-12	2	27
β-strand	17-25	9	26
β-strand	33-38	6	28
β-strand	46-52	7	28
β-strand	56-59	4	28
β-strand	67-72	6	26
β-strand	77-82A	7	26
α-helix	84-86	3
β-strand	88-90	3	29
β-strand	91-100A	11	28
β-strand	100J-100P	7	28
β-strand	105-107	3	29
β-strand	108-109	2	27
α-helix	112-114	3
β-strand	115	1	30
β-strand	118-119	2	31
β-strand	122	1	31
β-strand	133-143	11	31
β-strand	144	1	30
β-strand	149-152	4	32
α-helix	153-155	3
β-strand	161-163	3	31
α-helix	164-166	3
β-strand	174-183	10	31
β-strand	193-198	6	32
α-helix	199-201	3
β-strand	203-208	6	32

Chain L: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	4	33
β-strand	18-26	9	34
β-strand	31	1	35
β-strand	34-38	5	33
β-strand	44-48	5	33
β-strand	49	1	36
β-strand	53	1	36
β-strand	62-64	3	34
β-strand	70-76	7	34
α-helix	80-82	3
β-strand	85-89	5	33
β-strand	92	1	35
β-strand	97	1	28
α-helix	98-100	3
β-strand	102-106	5	33
β-strand	117-119	3	37
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-138	8	37
β-strand	146-151	6	38
β-strand	154-155	2	38
β-strand	160-162	3	37
α-helix	163-165	3
β-strand	166-167	2	37
β-strand	173-181	9	37
α-helix	183-186	4
β-strand	192-197	6	38
β-strand	202-207	6	38

Molecules and chains

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

Sequence of entity 1 (B), FASTA

>5U7O_1 Envelope glycoprotein gp160 (chains B)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (D), FASTA

>5U7O_2 35O22 FAB HEAVY CHAIN (chains D)
QGQLVQSGAELKKPGASVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVIMTTDTEVPVTSFTSTGAAYMEIRNLKFDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGLEV
LFQ

Sequence of entity 3 (E), FASTA

>5U7O_3 35O22 FAB LIGHT CHAIN (chains E)
QSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPGI
SPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQSKANPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (G), FASTA

>5U7O_4 Envelope glycoprotein gp160 (chains G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 5 (H), FASTA

>5U7O_5 PGT122 FAB HEAVY CHAIN (chains H)
QVHLQESGPGLVKPSETLSLTCNVSGTLVRDNYWSWIRQPLGKQPEWIGYVHDSGDTNYN
PSLKSRVHLSLDKSKNLVSLRLTGVTAADSAIYYCATTKHGRRIYGVVAFKEWFTYFYMD
VWGKGTSVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

Sequence of entity 6 (L), FASTA

>5U7O_6 PGT122 FAB LIGHT CHAIN (chains L)
APTFVSVAPGQTARITCGEESLGSRSVIWYQQRPGQAPSLIIYNNNDRPSGIPDRFSGSP
GSTFGTTATLTITSVEAGDEADYYCHIWDSRRPTNWVFGEGTTLIVLSQPKAAPSVTLFP
PSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLS
LTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
83J	1-[4-(benzenecarbonyl)piperazin-1-yl]-2-[4-methoxy-7-(3-methyl-1H-1,2,4-triazol…	C24 H23 N7 O4	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

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

Primary citation

Crystal structures of trimeric HIV envelope with entry inhibitors BMS-378806 and BMS-626529. Pancera, M., Lai, Y.T., Bylund, T. et al. Nat Chem Biol (2017) 13:1115-1122. DOI 10.1038/nchembio.2460 · 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…
4TVP 3.1 Å, Crystal Structure of the HIV-1 BG505 SOSIP.664 Env Trimer Ectodomain, Comprising…
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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