6W03: HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer

Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.3 Angstrom. Determined by X-ray diffraction at 2.4 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 10,096
Mol. weight: 156.59 kDa
Ligands: NAG
Released: 15 Apr 2020

Explore 6W03 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W03 contains 33 α-helices and 113 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
α-helix	530-533	4
α-helix	538-542	5
α-helix	571-594	24
β-strand	603-605	3	1
β-strand	606	1	2
β-strand	607-609	3	1
α-helix	610-611	2
α-helix	620-623	4
α-helix	628-634	7
α-helix	639-660	22

Chain D: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	3
β-strand	19-24	6	3
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	74	1	4
β-strand	77-82	6	3
β-strand	88-94	7	5
β-strand	102-103	2	5
β-strand	107-108	2	5

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-12	3	8
β-strand	19-24	6	7
β-strand	32-38	7	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-66	5	7
β-strand	70-75	6	7
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: 12 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	9
β-strand	53-56	4	10
β-strand	66-67	2	11
β-strand	75-76	2	10
α-helix	77-78	2
β-strand	83-86	4	9
β-strand	91-94	4	12
α-helix	100-114	15
α-helix	120	1
β-strand	121	1	13
β-strand	129-133	5	14
β-strand	154-162	9	14
β-strand	169-177	9	14
α-helix	178-180	3
β-strand	181-183	3	14
β-strand	190-193	4	14
α-helix	194-197	4
β-strand	201-203	3	13
α-helix	204-205	2
β-strand	208-209	2	11
β-strand	215	1	15
β-strand	216-218	3	10
α-helix	219-220	2
β-strand	223-228	6	9
β-strand	236-239	4	12
β-strand	242-245	4	9
β-strand	247	1	10
β-strand	251	1	15
β-strand	257	1	16
β-strand	259	1	16
β-strand	261	1	17
β-strand	271-272	2	17
β-strand	284-308	25	17
β-strand	316-323	9	17
β-strand	330-333	4	17
α-helix	335-353	19
β-strand	359-361	3	17
α-helix	369-372	4
β-strand	374-378	5	18
β-strand	381-385	5	18
α-helix	387-389	3
β-strand	393-394	2	17
β-strand	414-417	4	17
β-strand	418-421	4	18
β-strand	423-424	2	13
β-strand	433-435	3	13
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	9
β-strand	494-499	6	1
β-strand	502	1	2

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	11-12	2	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	33-39	7	21
β-strand	45-51	7	21
β-strand	57-59	3	21
β-strand	72	1	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-100A	14	21
β-strand	100J-101	10	21
β-strand	105-107	3	21
β-strand	108-109	2	20
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	161-163	3	23
α-helix	164-165	2
β-strand	167-168	2	23
β-strand	174-183	10	23
α-helix	184-186	3
β-strand	193-198	6	24
α-helix	199-201	3
β-strand	203-208	6	24

Chain L: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	25
β-strand	18-22	5	26
β-strand	31-38	8	25
β-strand	45-48	4	25
β-strand	62-64	3	26
β-strand	72-76	5	26
β-strand	85-92	8	25
β-strand	102-107	6	25
α-helix	109-111	3
β-strand	112	1	27
β-strand	117-119	3	28
α-helix	120-122	3
α-helix	123-126	4
β-strand	131-136	6	28
β-strand	137-140	4	29
β-strand	141	1	27
β-strand	145-151	7	30
β-strand	154-155	2	30
β-strand	160-162	3	28
β-strand	166-167	2	29
β-strand	173-175	3	29
β-strand	177-181	5	28
α-helix	183-187	5
β-strand	192-198	7	30
β-strand	201-207	7	30

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	134	Homo sapiens
35O22 scFv light chain	E	protein	114	Homo sapiens
Envelope glycoprotein gp160	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

Sequence of entity 1 (B), FASTA

>6W03_1 Envelope glycoprotein gp41 (chains B)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (D), FASTA

>6W03_2 35O22 scFv heavy chain (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVNMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSAST

Sequence of entity 3 (E), FASTA

>6W03_3 35O22 scFv light chain (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQS

Sequence of entity 4 (G), FASTA

>6W03_4 Envelope glycoprotein gp160 (chains G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNMTRKSIRIGPGQAFYALGDIIGDIRQPHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 5 (H), FASTA

>6W03_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ

Sequence of entity 6 (L), FASTA

>6W03_6 3H109L Fab light chain (chains L)
SVTSYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERF
SGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPMQWKMHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

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

Primary citation

Development of a 3Mut-Apex-Stabilized Envelope Trimer That Expands HIV-1 Neutralization Breadth When Used To Boost Fusion Peptide-Directed Vaccine-Elicited Responses. Chuang, G.Y., Lai, Y.T., Boyington, J.C. et al. J Virol (2020) 94. DOI 10.1128/JVI.00074-20 · 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…
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…
6NNJ 2.6 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to CH31 scFv in…
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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