6MUF: HIV-1 B41 SOSIP.664 Prefusion Env Trimer

Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.4 Angstrom. Determined by X-ray diffraction at 2.91 Å resolution. Released 16 Jan 2019.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 9,881
Mol. weight: 155.44 kDa
Ligands: NAG
Released: 16 Jan 2019

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

Secondary structure: helices and β-sheets

6MUF contains 30 α-helices and 122 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: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	529	1	1
α-helix	530-533	4
α-helix	539-542	4
α-helix	570-594	25
β-strand	603-609	7	2
α-helix	620-623	4
β-strand	627	1	1
α-helix	628-635	8
α-helix	639-660	22

Chain D: 2 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	3
β-strand	19-20	2	4
β-strand	22-24	3	3
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
α-helix	61-63	3
β-strand	67-71	5	4
β-strand	72C-72D	2	7
β-strand	74-75	2	7
β-strand	77	1	3
β-strand	78-82	5	4
β-strand	88-94	7	5
β-strand	102-103	2	5
β-strand	107-108	2	5

Chain E: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	8
β-strand	5-6	2	9
β-strand	9-12	3	10
β-strand	19-21	3	11
β-strand	23-24	2	9
β-strand	32-38	7	10
β-strand	45-49	5	10
β-strand	53-54	2	10
α-helix	55	1
β-strand	62-66	5	11
β-strand	71-75	5	11
α-helix	80-82	3
β-strand	84-91	8	10
β-strand	97-98	2	10
β-strand	99	1	8
β-strand	102-105	4	10

Chain G: 9 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	2
β-strand	45-47	3	12
β-strand	53-56	4	13
β-strand	66-67	2	14
α-helix	71-73	3
β-strand	75-76	2	13
β-strand	83-86	4	12
β-strand	91-94	4	15
α-helix	99-115	17
α-helix	120	1
β-strand	121	1	16
β-strand	129-132	4	17
β-strand	154-162	9	17
β-strand	169-177	9	17
α-helix	178-180	3
β-strand	181-183	3	17
β-strand	190-193	4	17
β-strand	200-203	4	16
α-helix	204-205	2
β-strand	208-209	2	14
β-strand	215	1	18
β-strand	216-218	3	13
α-helix	219-220	2
β-strand	223-226	4	12
β-strand	236-239	4	15
β-strand	242-245	4	12
β-strand	247	1	13
β-strand	251	1	18
β-strand	257	1	19
β-strand	259	1	19
β-strand	261	1	20
β-strand	271-273	3	20
β-strand	284-308	25	20
β-strand	316-323	9	20
β-strand	330-334	5	20
α-helix	335-351	17
β-strand	359-361	3	20
β-strand	374-375	2	21
β-strand	378	1	22
β-strand	381	1	22
β-strand	382-385	4	21
β-strand	393-395	3	20
β-strand	413-417	5	20
β-strand	418-421	4	21
β-strand	423-424	2	16
β-strand	432-435	4	16
α-helix	436-440	5
β-strand	441-456	16	20
β-strand	466-470	5	20
α-helix	476-480	5
β-strand	488-491	4	12
β-strand	494-499	6	2

Chain H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	23
β-strand	11-12	2	24
β-strand	18-25	8	23
α-helix	29-31	3
β-strand	33-39	7	25
β-strand	45-51	7	25
β-strand	59	1	25
β-strand	72	1	23
β-strand	77-82	6	23
α-helix	84-86	3
β-strand	88-100A	14	25
β-strand	100J-101	10	25
β-strand	105-107	3	25
β-strand	108-109	2	24
α-helix	113-114	2
β-strand	115	1	26
β-strand	119-122	4	27
β-strand	133-143	11	27
β-strand	144	1	26
β-strand	149-152	4	28
α-helix	153-155	3
β-strand	161	1	27
α-helix	163-165	3
β-strand	167-168	2	27
β-strand	174-183	10	27
α-helix	184-187	4
β-strand	193-198	6	28
α-helix	199-201	3
β-strand	203-208	6	28

Chain L: 4 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	29
β-strand	18-22	5	30
β-strand	31	1	31
β-strand	34-38	5	32
β-strand	45-48	4	32
β-strand	62-64	3	30
β-strand	72-76	5	30
β-strand	85-89	5	32
β-strand	92	1	31
β-strand	97	1	25
β-strand	102-107	6	29
α-helix	109-111	3
β-strand	112	1	33
β-strand	117-119	3	34
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-136	6	34
β-strand	137-140	4	35
β-strand	141	1	33
β-strand	145-151	7	36
β-strand	154-155	2	36
β-strand	160-162	3	34
β-strand	166-167	2	35
β-strand	173-175	3	35
β-strand	177-181	5	34
α-helix	183-188	6
β-strand	192-198	7	36
β-strand	201-207	7	36

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	B	protein	153	Human immunodeficiency virus 1	B3UEZ6
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	489	Human immunodeficiency virus 1	B3UES2
3H109L Fab heavy chain	H	protein	244	Homo sapiens
3H109L Fab light chain	L	protein	217	Homo sapiens

Sequence of entity 1 (B), FASTA

>6MUF_1 Envelope glycoprotein gp160 (chains B)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAPEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 2 (D), FASTA

>6MUF_2 35O22 scFv heavy chain portion (chains D)
QGQLVQSGATTTKPGSSVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVIMTTDTEVPVTSFTSTGAAYMEIRNLTSDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSAST

Sequence of entity 3 (E), FASTA

>6MUF_3 35O22 scFv light chain portion (chains E)
SQSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPG
ISPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQS

Sequence of entity 4 (G), FASTA

>6MUF_4 Envelope glycoprotein gp160 (chains G)
AAKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVT
ENFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDW
EKMETGEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTS
VITQACPKVSFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQL
LLNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATG
DIIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGE
FFYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIR
CSSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRR
VVQRRRRRR

Sequence of entity 5 (H), FASTA

>6MUF_5 3H109L Fab heavy chain (chains H)
QVQLQESGPGLVKPSETLSLTCTVSGGSISNYYWSWIRQSPGKGLEWIGYISDSESTNYN
PSLKSRVIISVDTSKNQLSLKLNSVTAADSAIYYCARAQQGKRIYGMVSFGEFFYYYYMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKGLE
VLFQ

Sequence of entity 6 (L), FASTA

>6MUF_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	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 B3UEZ6), best resolution first:

6MUG 2.95 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
6OKP 3.28 Å, B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody…
6OPN 3.5 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP in complex with small molecule GO35
6OPO 3.5 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
5VN8 3.6 Å, Cryo-EM model of B41 SOSIP.664 in complex with fragment antigen binding variable domain…
6X5B 3.6 Å, Symmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with small molecule…
5VN3 3.7 Å, Cryo-EM model of B41 SOSIP.664 in complex with soluble CD4 (D1-D2) and fragment antigen…
6OPP 3.7 Å, Asymmetric model of CD4- and 17-bound B41 HIV-1 Env SOSIP in complex with DDM
6OPQ 3.8 Å, CD4- and 17-bound HIV-1 Env B41 SOSIP frozen with LMNG
6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B
6X5C 4.04 Å, Asymmetric model of CD4-bound B41 HIV-1 Env SOSIP in complex with small molecule GO52
6EDU 4.06 Å, B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody…

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