6MDT: Transmembrane protein gp41

Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63 space group. Determined by X-ray diffraction at 3.82 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 3.82 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 6
Atoms: 12,314
Mol. weight: 182.8 kDa
Ligands: NAG
Released: 27 Feb 2019

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

Secondary structure: helices and β-sheets

6MDT contains 50 α-helices and 127 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: 9 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	539-542	4
α-helix	546-548	3
α-helix	570-594	25
β-strand	603-605	3	1
β-strand	606	1	2
β-strand	607-609	3	1
α-helix	619-625	7
α-helix	628-635	8
α-helix	639-647	9
α-helix	648-652	5
α-helix	653-661	9

Chain D: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
α-helix	7-9	3
β-strand	10-12	3	16
β-strand	17-27	11	15
β-strand	34-40	7	16
β-strand	44-51	8	16
β-strand	57-59	3	16
β-strand	67-71	5	15
β-strand	72C-72D	2	15
β-strand	74-82A	10	15
α-helix	84-86	3
β-strand	88-94	7	16
β-strand	102-103	2	16
β-strand	107-111	5	16
α-helix	115-116	2
β-strand	122-130	9	17
β-strand	135-145	11	17
β-strand	151-154	4	18
α-helix	155-157	3
β-strand	163-165	3	17
α-helix	166-168	3
β-strand	169-170	2	17
β-strand	176-185	10	17
β-strand	195-200	6	18
α-helix	201-203	3
β-strand	205-210	6	18
α-helix	211-212	2
α-helix	218-221	4

Chain E: 8 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	19
β-strand	9-13	5	20
β-strand	17-23	7	19
α-helix	26-28	3
β-strand	34-39	6	20
β-strand	47-50	4	20
β-strand	56	1	20
α-helix	57	1
β-strand	64-68	5	19
β-strand	72-78	7	19
α-helix	82-84	3
β-strand	87-93	7	20
β-strand	100-101	2	20
β-strand	105-110	6	20
α-helix	112-114	3
β-strand	118-122	5	21
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-141	8	21
β-strand	149-154	6	22
β-strand	158	1	22
β-strand	163-165	3	21
α-helix	166-168	3
β-strand	169-170	2	21
β-strand	176-184	9	21
α-helix	186-190	5
β-strand	195-200	6	22
β-strand	205-210	6	22

Chain G: 15 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-46	2	3
β-strand	53-55	3	4
β-strand	67	1	5
α-helix	75-78	4
β-strand	83-86	4	3
β-strand	91-94	4	6
α-helix	99-116	18
β-strand	121	1	7
α-helix	124-126	3
β-strand	129-132	4	8
α-helix	133-135	3
β-strand	156-162	7	8
β-strand	169-174	6	8
β-strand	175	1	9
α-helix	178-180	3
β-strand	181-183	3	8
β-strand	190-193	4	8
β-strand	201-203	3	7
α-helix	204-205	2
β-strand	209	1	5
β-strand	215	1	10
β-strand	216-218	3	4
α-helix	219-220	2
β-strand	223-227	5	3
β-strand	236-239	4	6
β-strand	242-245	4	3
β-strand	247	1	4
β-strand	251	1	10
β-strand	260-261	2	11
α-helix	264-266	3
β-strand	271-274	4	11
α-helix	283	1
β-strand	284-300	17	11
β-strand	301	1	12
β-strand	302	1	11
β-strand	304-312	7	9
β-strand	315-320	6	9
β-strand	323	1	12
β-strand	330-334	5	11
α-helix	335-351	17
α-helix	369-372	4
β-strand	374-379	6	13
β-strand	381-385	5	13
β-strand	413-417	5	11
β-strand	418-421	4	13
β-strand	423-424	2	7
α-helix	426-428	3
β-strand	433-435	3	7
α-helix	437-439	3
β-strand	441-454	14	11
β-strand	456	1	14
β-strand	468	1	14
α-helix	477-480	4
β-strand	486-491	6	3
β-strand	494-499	6	1
β-strand	502	1	2
α-helix	503-506	4

Chain H: 2 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	23
β-strand	11-12	2	24
β-strand	18-24	7	23
β-strand	33-39	7	25
β-strand	45-51	7	25
β-strand	57-59	3	25
β-strand	67-71	5	23
β-strand	77-82	6	23
β-strand	88-100A	14	25
β-strand	100J-101	10	25
β-strand	105-107	3	25
β-strand	108-109	2	24
β-strand	119-122	4	26
α-helix	130-132	3
β-strand	133-143	11	26
β-strand	149-152	4	27
β-strand	161-163	3	26
α-helix	164-166	3
β-strand	167-168	2	26
β-strand	174-183	10	26
β-strand	193-198	6	27
β-strand	203-208	6	27

Chain L: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	8	1
β-strand	9-14	6	28
β-strand	19-21	3	29
β-strand	31	1	30
β-strand	34-38	5	28
β-strand	45-48	4	28
β-strand	50	1	31
β-strand	53	1	31
β-strand	62-64	3	29
β-strand	73-75	3	29
α-helix	80-82	3
β-strand	85-89	5	28
β-strand	92	1	30
α-helix	98-101	4
β-strand	102-107	6	28
α-helix	109-111	3
β-strand	115-119	5	32
α-helix	120-122	3
α-helix	123-127	5
β-strand	131-140	10	32
β-strand	145-151	7	33
β-strand	154-155	2	33
β-strand	160-162	3	32
α-helix	163-165	3
β-strand	166-167	2	32
β-strand	173-181	9	32
α-helix	183-188	6
β-strand	192-198	7	33
β-strand	201-207	7	33

Molecules and chains

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

Sequence of entity 1 (B), FASTA

>6MDT_1 Transmembrane protein gp41 (chains B)
AVGLGAFILGFLGAAGSTMGAASMALTVQARLLLSGIVQQQNNLLRAIEAQQHMLQLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKIICCTNVPWNDSWSNKTINEIWDNMTWMQW
EKEIDNYTQHIYTLLEVSQIQQEKNEQELLELD

Sequence of entity 2 (G), FASTA

>6MDT_2 Surface protein gp120 (chains G)
AKKWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQEIVLGNVTE
NFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNCNNVNTNNTNNSTNATISDWE
KMETGEMKNCSFNVTTSIRDKIKKEYALFYKLDVVPLENKNNINNTNITNYRLINCNTSV
ITQACPKVSFEPIPIHYCAPAGFAILKCNSKTFNGSGPCTNVSTVQCTHGIRPVVSTQLL
LNGSLAEEEIVIRSENITDNAKTIIVQLNEAVEINCTRPNNNTRKSIHIGPGRAFYATGD
IIGNIRQAHCNISKARWNETLGQIVAKLEEQFPNKTIIFNHSSGGDPEIVTHSFNCGGEF
FYCNTTPLFNSTWNNTRTDDYPTGGEQNITLQCRIKQIINMWQGVGKAMYAPPIRGQIRC
SSNITGLLLTRDGGRDQNGTETFRPGGGNMRDNWRSELYKYKVVKIEPLGIAPTACKRRV
VQ

Sequence of entity 3 (D), FASTA

>6MDT_3 35O22 Fab heavy chain (chains D)
EGQLVQSGAELKKPGASVKISCKTSGYRFNFYHINWIRQTAGRGPEWMGWISPYSGDKNL
APAFQDRVIMTTDTEVPVTSFTSTGAAYMEIRNLKFDDTGTYFCAKGLLRDGSSTWLPYL
WGQGTLLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSG
VHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKGLEV
LFQ

Sequence of entity 4 (E), FASTA

>6MDT_4 35O22 Fab light chain (chains E)
QSVLTQSASVSGSLGQSVTISCTGPNSVCCSHKSISWYQWPPGRAPTLIIYEDNERAPGI
SPRFSGYKSYWSAYLTISDLRPEDETTYYCCSYTHNSGCVFGTGTKVSVLGQSKANPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 5 (H), FASTA

>6MDT_5 PGT124 Fab heavy chain (chains H)
QVQLQESGPGLVRPSETLSVTCIVSGGSISNYYWTWIRQSPGKGLEWIGYISDRETTTYN
PSLNSRAVISRDTSKNQLSLQLRSVTTADTAIYFCATARRGQRIYGVVSFGEFFYYYYMD
VWGKGTAVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD

Sequence of entity 6 (L), FASTA

>6MDT_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	9

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
6MCO 3.53 Å, Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P23…
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

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