6MCO: Transmembrane protein gp41

Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23 space group. Determined by X-ray diffraction at 3.53 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 3.53 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 12,268
Mol. weight: 182.2 kDa
Ligands: NAG
Released: 27 Feb 2019

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

Secondary structure: helices and β-sheets

6MCO contains 47 α-helices and 130 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: 8 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	519-522	4
α-helix	540-543	4
α-helix	570-594	25
β-strand	603-609	7	1
α-helix	619-623	5
α-helix	628-635	8
α-helix	639-646	8
α-helix	647-652	6
α-helix	653-661	9

Chain D: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	2
β-strand	10-12	3	3
β-strand	17-25	9	2
β-strand	34-40	7	3
β-strand	44-51	8	3
β-strand	57-59	3	3
β-strand	67-71	5	2
α-helix	72-72B	3
β-strand	72C-72D	2	4
β-strand	74-75	2	4
β-strand	76-82A	8	2
α-helix	84-86	3
β-strand	88-94	7	3
β-strand	102-103	2	3
α-helix	104	1
β-strand	107-111	5	3
β-strand	120-130	11	5
β-strand	135-145	11	5
β-strand	151-154	4	6
α-helix	155-157	3
β-strand	159	1	6
β-strand	163-165	3	5
α-helix	166-168	3
β-strand	169-170	2	5
β-strand	176-185	10	5
β-strand	195-200	6	6
β-strand	205-210	6	6
α-helix	218-221	4

Chain E: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	7
β-strand	9-14	5	8
β-strand	18-24	7	7
α-helix	27-27B	3
β-strand	32-37	6	8
α-helix	43-44	2
β-strand	45-48	4	8
α-helix	53	1
β-strand	54	1	8
α-helix	55	1
β-strand	62-66	5	7
β-strand	71-76	6	7
α-helix	80-82	3
β-strand	85-91	7	8
β-strand	98	1	8
β-strand	102-106A	6	8
β-strand	114-118	5	9
α-helix	119-121	3
α-helix	122-126	5
β-strand	130-137	8	9
β-strand	145-150	6	10
β-strand	154	1	10
β-strand	159-161	3	9
α-helix	162-164	3
β-strand	165-166	2	9
β-strand	172-180	9	9
α-helix	182-186	5
β-strand	191-196	6	10
β-strand	201-206	6	10

Chain G: 15 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-47	3	11
β-strand	53	1	12
β-strand	55-56	2	13
β-strand	75-76	2	13
α-helix	77-78	2
β-strand	83-86	4	11
β-strand	91-92	2	14
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	15
α-helix	123-125	3
β-strand	129	1	16
β-strand	130-132	3	17
β-strand	156-162	7	17
β-strand	169-174	6	17
α-helix	178-180	3
β-strand	181-183	3	16
β-strand	191-193	3	16
β-strand	201-203	3	15
α-helix	204-205	2
β-strand	215	1	18
β-strand	218	1	12
α-helix	219-220	2
β-strand	221	1	11
β-strand	223-228	6	11
β-strand	238-239	2	14
β-strand	242-245	4	11
β-strand	247	1	12
β-strand	251	1	18
β-strand	256	1	19
β-strand	259-261	3	20
α-helix	264-266	3
β-strand	271-274	4	21
β-strand	284-287	4	21
α-helix	291	1
β-strand	292-300	9	20
β-strand	301	1	22
β-strand	302	1	20
β-strand	304-312	7	23
β-strand	315-320	6	23
β-strand	323	1	22
β-strand	329-334	6	20
α-helix	335-352	18
β-strand	374-378	5	19
β-strand	381-385	5	19
α-helix	412	1
β-strand	413-418	6	20
β-strand	419-421	3	19
β-strand	423-424	2	15
α-helix	426-428	3
β-strand	433-435	3	15
α-helix	436-438	3
β-strand	441-452	12	20
β-strand	453-454	2	21
β-strand	456	1	24
β-strand	468	1	24
α-helix	477-480	4
β-strand	486-491	6	11
β-strand	494-499	6	1
α-helix	503-506	4

Chain H: 4 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	25
β-strand	11-12	2	26
β-strand	18-24	7	25
β-strand	33-39	7	27
β-strand	45-51	7	27
β-strand	57-59	3	27
β-strand	67-72	6	25
β-strand	77-82	6	25
β-strand	88-100A	14	27
β-strand	100J-101	10	27
β-strand	105-107	3	27
β-strand	108-109	2	26
α-helix	112-114	3
β-strand	119-122	4	28
β-strand	129	1	28
β-strand	133-140	8	28
β-strand	143	1	29
β-strand	149-152	4	30
α-helix	153-155	3
β-strand	161-163	3	28
α-helix	164-166	3
β-strand	174	1	29
β-strand	177-183	7	28
α-helix	184-186	3
β-strand	193-197	5	30
β-strand	204-208	5	30

Chain L: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	31
β-strand	19-21	3	32
β-strand	31	1	33
β-strand	34-38	5	31
β-strand	45-48	4	31
β-strand	63-64	2	32
β-strand	73-75	3	32
α-helix	80-82	3
β-strand	85-89	5	31
β-strand	92	1	33
α-helix	98-101	4
β-strand	102-107	6	31
β-strand	115-119	5	34
α-helix	123-127	5
β-strand	131-140	10	34
β-strand	146-151	6	35
β-strand	154-155	2	35
β-strand	160-162	3	34
α-helix	163-165	3
β-strand	166-167	2	34
β-strand	173-181	9	34
α-helix	183-188	6
β-strand	192-198	7	35
β-strand	201-207	7	35

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transmembrane protein gp41	B	protein	153	Human immunodeficiency virus 1	B3UES2
35O22 Fab heavy chain	D	protein	243	Homo sapiens
35O22 Fab light chain	E	protein	216	Homo sapiens
Surface protein gp120	G	protein	482	Human immunodeficiency virus 1	B3UF58
PGT124 Fab heavy chain	H	protein	236	Homo sapiens
PGT124 Fab light chain	L	protein	214	Homo sapiens

Sequence of entity 1 (B), FASTA

>6MCO_1 Transmembrane protein gp41 (chains B)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAIEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 2 (D), FASTA

>6MCO_2 35O22 Fab heavy chain (chains D)
EGQLVQSGAELKKPGASVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVIMTTDTEVPVTSFTSTGAAYMEIRNLKFDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGLEV
LFQ

Sequence of entity 3 (E), FASTA

>6MCO_3 35O22 Fab light chain (chains E)
QSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPGI
SPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQSKANPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (G), FASTA

>6MCO_4 Surface protein gp120 (chains G)
AKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTE
NFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWE
KMETGEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSV
ITQACPKVSFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLL
LNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGD
IIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEF
FYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRC
SSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV
VQ

Sequence of entity 5 (H), FASTA

>6MCO_5 PGT124 Fab heavy chain (chains H)
QVQLQESGPGLVRPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYN
PSLNSRAVISRDTSKNQLSLQLRSVTTADTAIYFCATARRGQRIYGVVSFGEFFYYYYMD
VWGKGTAVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 6 (L), FASTA

>6MCO_6 PGT124 Fab light chain (chains L)
SYVSPLSVALGETARISCGRQALGSRAVQWYQHKPGQAPILLIYNNQDRPSGIPERFSGT
PDINFGTTATLTISGVEVGDEADYYCHMWDSRSGFSWSFGGATRLTVLSQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHKSYSCQVTHEGSTVEKTVAPTECS

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide. Kumar, S., Sarkar, A., Pugach, P. et al. Nat Commun (2019) 10:763-763. DOI 10.1038/s41467-019-08738-5 · PubMed

Other PDB entries of the same protein (UniProt B3UES2), best resolution first:

6MUF 2.91 Å, Crystal Structure of HIV-1 B41 SOSIP.664 Prefusion Env Trimer in Complex with Human…
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
6MDT 3.82 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63…
6U59 3.86 Å, HIV-1 B41 SOSIP.664 in complex with rabbit antibody 13B

Browse structure collections

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