6CM3: BG505 SOSIP

BG505 SOSIP in complex with sCD4, 17b, 8ANC195. Determined by electron microscopy at 3.54 Å resolution. Released 17 Oct 2018.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 21
Atoms: 25,455
Mol. weight: 587.36 kDa
Ligands: NAG
Released: 17 Oct 2018

Explore 6CM3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6CM3 contains 72 α-helices and 268 β-strands across 21 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.

Chains A and B: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	521-525	5
α-helix	530-543	14
α-helix	566-592	27
β-strand	603	1	1
β-strand	609	1	2
α-helix	619-625	7
α-helix	628-634	7
α-helix	635-637	3
α-helix	639-648	10

Chain C: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	521-525	5
α-helix	530-543	14
α-helix	566-592	27
β-strand	609	1	5
α-helix	619-625	7
α-helix	628-634	7
α-helix	635-637	3
α-helix	639-648	10

Chains D and E: 8 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	4
β-strand	39	1	3
α-helix	65-73	9
β-strand	84-85	2	6
β-strand	91-92	2	7
α-helix	95-97	3
α-helix	101-115	15
β-strand	120-123	4	8
β-strand	127	1	9
β-strand	195	1	9
β-strand	199-202	4	8
α-helix	212-214	3
β-strand	215	1	10
β-strand	218	1	11
β-strand	223-228	6	6
β-strand	238-239	2	7
β-strand	242-245	4	6
β-strand	247	1	11
β-strand	251	1	10
β-strand	256	1	12
β-strand	259-261	3	13
β-strand	271-273	3	13
β-strand	284-298	15	13
β-strand	329-333	5	13
α-helix	338-353	16
β-strand	358	1	14
α-helix	369-372	4
β-strand	375-378	4	12
β-strand	381-384	4	12
β-strand	414-418	5	13
β-strand	419-420	2	12
β-strand	423-425	3	8
α-helix	426	1
β-strand	432-434	3	8
β-strand	443-454	12	13
β-strand	466	1	14
β-strand	470	1	13
α-helix	476-479	4
β-strand	486-490	5	6

Chain F: 8 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	35	1	5
α-helix	65-73	9
β-strand	84-85	2	24
β-strand	91-92	2	25
α-helix	95-97	3
α-helix	101-115	15
β-strand	120-123	4	26
β-strand	127	1	27
β-strand	195	1	27
β-strand	199-202	4	26
α-helix	212-214	3
β-strand	215	1	28
β-strand	218	1	29
β-strand	223-228	6	24
β-strand	238-239	2	25
β-strand	242-245	4	24
β-strand	247	1	29
β-strand	251	1	28
β-strand	256	1	30
β-strand	259-261	3	31
β-strand	271-273	3	31
β-strand	284-298	15	31
β-strand	329-333	5	31
α-helix	338-353	16
β-strand	358	1	32
α-helix	369-372	4
β-strand	375-378	4	30
β-strand	381-384	4	30
β-strand	414-418	5	31
β-strand	419-420	2	30
β-strand	423-425	3	26
α-helix	426	1
β-strand	432-434	3	26
β-strand	443-454	12	31
β-strand	466	1	32
β-strand	470	1	31
α-helix	476-479	4
β-strand	486-490	5	24

Chains G, H and I: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	33
β-strand	12-17	6	34
β-strand	27-29	3	33
β-strand	35-40	6	33
β-strand	43-45	3	33
β-strand	55-56	2	34
α-helix	59-64	6
β-strand	66-71	6	34
β-strand	81-85	5	33
β-strand	91-96	6	33

Chains J, L and N: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	39
β-strand	10	1	40
α-helix	18-19	2
β-strand	21-24	4	39
β-strand	33-38	6	40
β-strand	45-49	5	40
β-strand	53-54	2	40
β-strand	62-67	6	39
β-strand	70-75	6	39
β-strand	85-90	6	40
β-strand	100	1	40
β-strand	104-105	2	40

Chains K, M and O: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	41
α-helix	7-9	3
β-strand	10-12	3	42
β-strand	18-20	3	41
β-strand	22-25	4	41
α-helix	29-31	3
β-strand	32-39	8	42
β-strand	45-52	8	42
β-strand	57-60	4	42
β-strand	68-73	6	41
β-strand	78-83	6	41
α-helix	88-90	3
β-strand	92-100	9	42
β-strand	117-118	2	42
β-strand	122-126	5	42

Chains P, R and T: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	51
β-strand	10-12	3	52
β-strand	18-23	6	51
β-strand	33-40	8	52
β-strand	46-51	6	52
α-helix	53-55	3
β-strand	58-59	2	52
β-strand	67-72	6	51
β-strand	81-86	6	51
β-strand	95-103	9	52
β-strand	112-113	2	53
β-strand	116-117	2	53
β-strand	121-122	2	52
β-strand	126-130	5	52

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Envelope glycoprotein gp160	A, B, C	protein	153	Human immunodeficiency virus 1	Q2N0S7
Envelope glycoprotein gp160	D, E, F	protein	481	Human immunodeficiency virus 1	Q2N0S5
T-cell surface glycoprotein CD4	G, H, I	protein	192	Homo sapiens	P01730 (AlphaFold model)
17b Fab light chain	J, L, N	protein	214	Homo sapiens
17b Fab heavy chain	K, M, O	protein	229	Homo sapiens
8ANC195 Fab heavy chain	P, R, T	protein	244	Homo sapiens
8ANC195 Fab light chain	Q, S, U	protein	215	Homo sapiens

Sequence of entity 1 (A, B, C), FASTA

>6CM3_1 Envelope glycoprotein gp160 (chains A, B, C)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 2 (D, E, F), FASTA

>6CM3_2 Envelope glycoprotein gp160 (chains D, E, F)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 3 (G, H, I), FASTA

>6CM3_3 T-cell surface glycoprotein CD4 (chains G, H, I)
KKVVLGKKGDTVELTCTASQKKSIQFHWKNSNQIKILGNQGSFLTKGPSKLNDRADSRRS
LWDQGNFPLIIKNLKIEDSDTYICEVEDQKEEVQLLVFGLTANSDTHLLQGQSLTLTLES
PPGSSPSVQCRSPRGKNIQGGKTLSVSQLELQDSGTWTCTVLQNQKKVEFKIDIVVLAFQ
KAIDGRHHHHHH

Sequence of entity 4 (J, L, N), FASTA

>6CM3_4 17b Fab light chain (chains J, L, N)
DIVMTQSPATLSVSPGERATLSCRASESVSSDLAWYQQKPGQAPRLLIYGASTRATGVPA
RFSGSGSGAEFTLTISSLQSEDFAVYYCQQYNNWPPRYTFGQGTRLEIKRTVAAPSVFIF
PPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSST
LTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Sequence of entity 5 (K, M, O), FASTA

>6CM3_5 17b Fab heavy chain (chains K, M, O)
EVQLVESGAEVKKPGSSVKVSCKASGDTFIRYSFTWVRQAPGQGLEWMGRIITILDVAHY
APHLQGRVTITADKSTSTVYLELRNLRSDDTAVYFCAGVYEGEADEGEYDNNGFLKHWGQ
GTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHT
FPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Sequence of entity 6 (P, R, T), FASTA

>6CM3_6 8ANC195 Fab heavy chain (chains P, R, T)
QIHLVQSGTEVKKPGSSVTVSCKAYGVNTFGLYAVNWVRQAPGQSLEYIGQIWRWKSSAS
HHFRGRVLISAVDLTGSSPPISSLEIKNLTSDDTAVYFCTTTSTYDKWSGLHHDGVMAFS
SWGQGTLISVSAASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHH
HHHH

Sequence of entity 7 (Q, S, U), FASTA

>6CM3_7 8ANC195 Fab light chain (chains Q, S, U)
DIQMTQSPSTLSASIGDTVRISCRASQSITGNWVAWYQQRPGKAPRLLIYRGAALLGGVP
SRFSGSAAGTDFTLTIGNLQAEDFGTFYCQQYDTYPGTFGQGTKVEVKRTVAAPSVFIFP
PSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTL
TLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	18

Primary citation

Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion. Wang, H., Barnes, C.O., Yang, Z. et al. Cell Host Microbe (2018) 24:579-592.e4. DOI 10.1016/j.chom.2018.09.003 · PubMed

Other PDB entries of the same protein (UniProt Q2N0S7), best resolution first:

5I8C 1.54 Å, Crystal Structure of HIV-1 Clade A BG505 Fusion Peptide (residue 512-520) in Complex…
6WX2 2.39 Å, Vaccine-elicited mouse FP-targeting neutralizing antibody vFP16.02 with F60P mutation on…
8FR6 2.5 Å, Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
8G4T 2.81 Å, Vaccine-elicited human antibody 2C09 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6V8Z 2.9 Å, VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure
8G4M 2.95 Å, Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP
6MPG 3.2 Å, Cryo-EM structure at 3.2 A resolution of HIV-1 fusion peptide-directed antibody,…
6UM7 3.5 Å, Cryo-EM structure of vaccine-elicited HIV-1 neutralizing antibody DH270.mu1 in complex…
9PNN 3.5 Å, Cryo-EM structure of J601-A6 Fab in complex with HIV-1 BG505 DS-SOSIP Env trimer
6CDI 3.6 Å, Cryo-EM structure at 3.6 A resolution of vaccine-elicited antibody vFP16.02 in complex…
8DOW 3.69 Å, Cryo-EM structure of HIV-1 Env(CH848 10.17 DS.SOSIP_DT) in complex with DH1030.1 Fab
7LL1 3.73 Å, Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly…

Browse structure collections

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