6MTN: 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 Compound 484 in Complex with Human Antibodies 3H109L and 35O22 at 3.0 Angstrom. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 10,157
Mol. weight: 156.33 kDa
Ligands: JYJ, NAG
Released: 16 Jan 2019

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

Secondary structure: helices and β-sheets

6MTN contains 36 α-helices and 115 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	538-541	4
α-helix	542-544	3
α-helix	570-595	26
β-strand	603-609	7	2
α-helix	619-623	5
β-strand	627	1	1
α-helix	628-634	7
α-helix	639-660	22

Chain D: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	3
β-strand	19-20	2	3
β-strand	22-27	6	3
α-helix	29-31	3
β-strand	34-40	7	4
β-strand	46-51	6	4
β-strand	57-59	3	4
α-helix	61-63	3
β-strand	67-72D	10	3
β-strand	74-82	9	3
β-strand	88-94	7	4
β-strand	102-103	2	4
β-strand	104	1	3
β-strand	107-108	2	4

Chain E: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	5
β-strand	9	1	6
β-strand	19-21	3	7
β-strand	23-24	2	5
β-strand	32-38	7	6
β-strand	45-48	4	6
β-strand	49	1	8
β-strand	53	1	8
α-helix	54-55	2
β-strand	62-66	5	7
β-strand	70	1	5
β-strand	71-75	5	7
α-helix	80-82	3
β-strand	85-91	7	6
β-strand	102-103	2	6

Chain G: 12 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-47	3	9
α-helix	51-52	2
β-strand	53-56	4	10
β-strand	67	1	11
α-helix	71-73	3
β-strand	75-76	2	10
α-helix	77-78	2
β-strand	83-85	3	9
β-strand	91-94	4	12
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	13
α-helix	123-125	3
β-strand	129-133	5	14
α-helix	140-153	6
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
β-strand	200-203	4	13
β-strand	209	1	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	259-261	3	14
β-strand	271-273	3	14
β-strand	284-312	27	14
β-strand	315-323	10	14
β-strand	330-334	5	14
α-helix	335-350	16
β-strand	359-361	3	14
β-strand	374-378	5	16
β-strand	381-385	5	16
β-strand	393-395	3	14
β-strand	413-417	5	14
β-strand	418-421	4	16
β-strand	423-425	3	13
β-strand	432-435	4	13
α-helix	437-440	4
β-strand	441-456	16	14
β-strand	466-470	5	14
α-helix	476-483	8
β-strand	488-491	4	9
β-strand	494-499	6	2

Chain H: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	17
β-strand	11-12	2	18
β-strand	18-25	8	17
β-strand	33-39	7	19
β-strand	46-51	6	19
β-strand	57-59	3	19
α-helix	64-66	3
β-strand	67-69	3	17
β-strand	72	1	17
β-strand	77-82	6	17
α-helix	84-86	3
β-strand	88-100A	14	19
β-strand	100J-101	10	19
β-strand	105-107	3	19
β-strand	108-109	2	18
α-helix	113-114	2
β-strand	115	1	20
β-strand	120-122	3	21
β-strand	133-143	11	21
β-strand	144	1	20
β-strand	149-150	2	22
β-strand	152	1	23
α-helix	153-155	3
β-strand	157	1	23
β-strand	161-163	3	21
α-helix	164-165	2
β-strand	167-168	2	21
β-strand	174-183	10	21
α-helix	184-187	4
β-strand	192-193	2	24
β-strand	196-198	3	22
α-helix	199-201	3
β-strand	203-205	3	22
β-strand	208-209	2	24

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	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	67C	1	27
β-strand	69	1	27
β-strand	72-76	5	26
α-helix	80-82	3
β-strand	84-92	9	25
β-strand	101-107	7	25
α-helix	109-111	3
β-strand	112	1	28
β-strand	117-119	3	29
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	29
β-strand	141	1	28
β-strand	145-151	7	30
β-strand	154-156	3	30
β-strand	160-162	3	29
α-helix	163-165	3
β-strand	166-167	2	29
β-strand	173-181	9	29
α-helix	184-187	4
β-strand	192-198	7	30
β-strand	201-207	7	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	B	protein	153	Human immunodeficiency virus 1	Q2N0S6
35O22 scFv heavy chain portion	D	protein	134	Homo sapiens
35O22 scFv light chain portion	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

>6MTN_1 Envelope glycoprotein gp160 (chains B)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (D), FASTA

>6MTN_2 35O22 scFv heavy chain portion (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVNMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSAST

Sequence of entity 3 (E), FASTA

>6MTN_3 35O22 scFv light chain portion (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQS

Sequence of entity 4 (G), FASTA

>6MTN_4 Envelope glycoprotein gp160 (chains G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNAITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 5 (H), FASTA

>6MTN_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ

Sequence of entity 6 (L), FASTA

>6MTN_6 3H109L Fab light chain (chains L)
SVTSYVRPLSVALGETASISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERF
SGTPDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSV
TLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAAS
SYLSLTPMQWKMHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
JYJ	{4-[1-(3-chlorophenyl)cyclopropane-1-carbonyl]piperazin-1-yl}(thiophen-3-yl)met…	C19 H19 Cl N2 O2 S	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	11

Primary citation

Lattice engineering enables definition of molecular features allowing for potent small-molecule inhibition of HIV-1 entry. Lai, Y.T., Wang, T., O'Dell, S. et al. Nat Commun (2019) 10:47-47. DOI 10.1038/s41467-018-07851-1 · 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…
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

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