6NNJ: HIV-1 BG505 SOSIP.664 Prefusion Env Trimer

Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in Complex with Crystallization Chaperones 3H109L Fab and 35O22 scFv at 3.1 Angstrom. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 8
Atoms: 11,874
Mol. weight: 186.24 kDa
Ligands: NAG
Released: 27 Feb 2019

Explore 6NNJ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NNJ contains 41 α-helices and 139 β-strands across 8 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, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-526	3
α-helix	530-533	4
α-helix	537-542	6
α-helix	570-594	25
β-strand	603-609	7	1
α-helix	620-623	4
α-helix	628-634	7
α-helix	639-660	22

Chain D: 1 helix, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	2
β-strand	19-20	2	3
β-strand	22-24	3	2
β-strand	27	1	4
α-helix	29-31	3
β-strand	34-40	7	5
β-strand	41	1	6
β-strand	43	1	6
β-strand	45-51	7	5
β-strand	57-59	3	5
β-strand	67-71	5	3
β-strand	72C-72D	2	4
β-strand	74-75	2	4
β-strand	77	1	2
β-strand	78-82	5	3
β-strand	88-94	7	5
β-strand	102-103	2	5
β-strand	107-108	2	5

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-12	3	8
β-strand	19-21	3	9
β-strand	24	1	7
β-strand	32-38	7	8
β-strand	46-49	4	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-66	5	9
β-strand	70	1	7
β-strand	71-75	5	9
α-helix	80-82	3
β-strand	84-91	8	8
β-strand	97-98	2	8
β-strand	102-105	4	8

Chain G: 13 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	10
β-strand	53-56	4	11
β-strand	67	1	12
α-helix	71-73	3
β-strand	75-76	2	11
α-helix	77-78	2
β-strand	83-86	4	10
β-strand	91-94	4	13
α-helix	99-114	16
α-helix	120	1
β-strand	121	1	14
α-helix	123-125	3
β-strand	129-133	5	15
β-strand	155-162	8	15
β-strand	169-176	8	15
α-helix	178-180	3
β-strand	181-183	3	15
β-strand	189-193	5	15
α-helix	194-197	4
β-strand	200-203	4	14
α-helix	204-205	2
β-strand	209	1	12
β-strand	215	1	16
β-strand	216-218	3	11
β-strand	223-226	4	10
β-strand	236-239	4	13
β-strand	242-245	4	10
β-strand	247	1	11
β-strand	251	1	16
β-strand	259-261	3	17
α-helix	270	1
β-strand	271-273	3	17
β-strand	284-302	19	17
β-strand	304-312	7	15
β-strand	315-320	6	15
β-strand	329-333	5	17
α-helix	335-353	19
β-strand	359-361	3	17
α-helix	369-372	4
β-strand	374-378	5	17
β-strand	381-385	5	17
β-strand	393-395	3	17
β-strand	414-421	8	17
β-strand	423-424	2	14
β-strand	432-435	4	14
α-helix	436-440	5
β-strand	441-456	16	17
β-strand	466-470	5	17
α-helix	476-483	8
β-strand	488-491	4	10
β-strand	494-499	6	1

Chain H: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	11-12	2	19
β-strand	17-25	9	18
α-helix	29-31	3
β-strand	33-39	7	20
β-strand	45-51	7	20
β-strand	57-59	3	20
β-strand	71-72	2	18
β-strand	77-82A	7	18
α-helix	84-86	3
β-strand	88-100A	14	20
α-helix	100E-100G	3
β-strand	100J-101	10	20
β-strand	105-107	3	20
β-strand	108-109	2	19
α-helix	113-114	2
β-strand	115	1	21
β-strand	119-122	4	22
β-strand	133-143	11	22
β-strand	144	1	21
β-strand	149-152	4	23
α-helix	153-155	3
β-strand	157	1	23
β-strand	161-163	3	22
α-helix	164-165	2
β-strand	168	1	22
β-strand	174-183	10	22
α-helix	185-187	3
β-strand	193-198	6	23
α-helix	199-201	3
β-strand	203-208	6	23

Chain L: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	24
β-strand	18-22	5	25
β-strand	31-38	8	24
β-strand	45-48	4	24
β-strand	50	1	26
β-strand	53	1	26
β-strand	62-64	3	25
β-strand	72-76	5	25
α-helix	80-82	3
β-strand	85-92	8	24
β-strand	101-107	7	24
β-strand	112	1	27
β-strand	115-119	5	28
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-140	10	28
β-strand	141	1	27
β-strand	145-151	7	29
β-strand	154-155	2	29
β-strand	160-162	3	28
β-strand	166-167	2	28
β-strand	173-175	3	28
β-strand	177-181	5	28
α-helix	183-187	5
β-strand	192-198	7	29
β-strand	201-207	7	29

Chain U: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4	1	30
β-strand	5-6	2	31
α-helix	7-9	3
β-strand	10-12	3	32
β-strand	18-23	6	31
α-helix	31E-34	7
β-strand	35-39	6	32
β-strand	45-51	7	32
β-strand	57-59	3	32
α-helix	61-63	3
β-strand	67-71	5	31
β-strand	78-82	5	31
α-helix	84-86	3
β-strand	88-94	7	32
β-strand	102-103	2	32
β-strand	104	1	30
β-strand	107-111	5	32

Chain V: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	33
β-strand	10-11	2	34
β-strand	19-25	7	33
β-strand	34-38	5	34
β-strand	45-49	5	34
β-strand	53-54	2	34
α-helix	55	1
β-strand	62-67	6	33
β-strand	70-75	6	33
β-strand	85-90	6	34
β-strand	97-98	2	34
β-strand	102-104	3	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp41	B	protein	153	Human immunodeficiency virus 1	Q2N0S6
35O22 scFv heavy chain	D	protein	153	Homo sapiens
35O22 scFv light chain	E	protein	130	Homo sapiens
Envelope glycoprotein gp120	G	protein	481	Human immunodeficiency virus 1	Q2N0S6
3H109L Fab heavy chain	H	protein	244	Homo sapiens
3H109L Fab light chain	L	protein	217	Homo sapiens
CH31 scFv heavy chain	U	protein	137	Homo sapiens
CH31 scFv light chain	V	protein	117	Homo sapiens

Sequence of entity 1 (B), FASTA

>6NNJ_1 Envelope glycoprotein gp41 (chains B)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (D), FASTA

>6NNJ_2 35O22 scFv heavy chain (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVNMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSASTGGGGSGGGGSGGGGSGGGG

Sequence of entity 3 (E), FASTA

>6NNJ_3 35O22 scFv light chain (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQSGGLVPR
GSHHHHHHHH

Sequence of entity 4 (G), FASTA

>6NNJ_4 Envelope glycoprotein gp120 (chains G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 5 (H), FASTA

>6NNJ_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ

Sequence of entity 6 (L), FASTA

>6NNJ_6 3H109L Fab light chain (chains L)
SVTSYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERF
SGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPMQWKMHKSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 7 (U), FASTA

>6NNJ_7 CH31 scFv heavy chain (chains U)
QVQLVQSGAAVRKPGASVTVSCKFAEDDDYSPYWVNPAPEHFIHFLRQAPGQQLEWLAWM
NPTNGAVNYAWYLNGRVTATRDRSMTTAFLEVKSLRSDDTAVYYCARAQKRGRSEWAYAH
WGQGTPVVVSSGGLVPR

Sequence of entity 8 (V), FASTA

>6NNJ_8 CH31 scFv light chain (chains V)
DIQMTQSPSSLSASLGDRVTITCQASRGIGKDLNWYQQKAGKAPKLLVSDASTLEGGVPS
RFSGSGFHQNFSLTISSLQAEDVATYFCQQYETFGQGTKVDIGGGGSGGGGSGGGGS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	7

Primary citation

Improvement of antibody functionality by structure-guided paratope engraftment. Liu, Q., Lai, Y.T., Zhang, P. et al. Nat Commun (2019) 10:721-721. DOI 10.1038/s41467-019-08658-4 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S6), best resolution first:

8TOX 2.3 Å, Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
6MTJ 2.34 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6W03 2.4 Å, Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with…
6MTN 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6UDJ 2.5 Å, HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MU7 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6MU6 2.55 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
8EUV 2.6 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-COMBO1 FAB
8T4K 2.6 Å, MD64 N332-GT5 sosip
8EUU 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01 FAB
8EUW 2.7 Å, Cryo-EM structure of HIV-1 BG505 DS-SOSIP ENV trimer bound to VRC34.01-MM28 FAB

Browse structure collections

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