7LL1: BG505 DS-SOSIP

Cryo-EM structure of BG505 DS-SOSIP in complex with glycan276-dependent broadly neutralizing antibody VRC40.01 Fab. Determined by electron microscopy at 3.73 Å resolution. Released 17 Mar 2021.

Method: Electron microscopy
Resolution: 3.73 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 12
Atoms: 25,773
Mol. weight: 376.01 kDa
Ligands: NAG
Released: 17 Mar 2021

Explore 7LL1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LL1 contains 123 α-helices and 257 β-strands across 12 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 A: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	35-39	5	1
β-strand	45-47	3	2
β-strand	53-55	3	3
β-strand	56	1	4
α-helix	58-62	5
β-strand	76	1	4
α-helix	77-78	2
β-strand	84-86	3	2
β-strand	91-94	4	5
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	6
α-helix	123-125	3
β-strand	129-133	5	7
β-strand	154-162	9	7
β-strand	169-177	9	7
α-helix	178-180	3
β-strand	181-183	3	7
β-strand	190-193	4	7
α-helix	194-197	4
β-strand	201-203	3	6
α-helix	204-205	2
β-strand	216-218	3	3
α-helix	219-220	2
β-strand	223-228	6	2
β-strand	236-239	4	5
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	256	1	8
β-strand	259-261	3	9
α-helix	264-266	3
β-strand	271-273	3	9
β-strand	284-312	27	9
β-strand	315-323	10	9
β-strand	330-334	5	9
α-helix	335-352	18
β-strand	360-361	2	9
α-helix	369-372	4
β-strand	374-377	4	8
β-strand	382-385	4	8
β-strand	394	1	9
β-strand	413-417	5	9
β-strand	418-421	4	8
β-strand	423-425	3	6
β-strand	433-435	3	6
α-helix	436-438	3
β-strand	441-456	16	9
β-strand	467-470	4	9
α-helix	476-482	7
β-strand	486-491	6	2
β-strand	495-499	5	1

Chain B: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	518-520	3
β-strand	529	1	10
α-helix	530-533	4
α-helix	537-542	6
α-helix	546-548	3
α-helix	549-552	4
α-helix	567-570	4
α-helix	573-595	23
β-strand	603-609	7	1
α-helix	619-624	6
β-strand	627	1	10
α-helix	628-635	8
α-helix	639-662	24

Chain C: 16 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	11
β-strand	45-47	3	12
β-strand	53-56	4	13
α-helix	58-62	5
β-strand	68	1	14
β-strand	76	1	13
α-helix	77-78	2
β-strand	84-85	2	12
β-strand	91-94	4	15
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	16
α-helix	123-125	3
β-strand	129-133	5	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
α-helix	194-197	4
β-strand	201-203	3	16
α-helix	204-205	2
β-strand	209	1	14
β-strand	215-218	4	13
α-helix	219-220	2
β-strand	223-228	6	12
β-strand	236-239	4	15
β-strand	242-245	4	12
β-strand	247	1	13
β-strand	251	1	13
β-strand	256	1	18
β-strand	259-261	3	17
β-strand	271-273	3	17
β-strand	284-312	27	17
β-strand	315-323	10	17
β-strand	330-334	5	17
α-helix	335-352	18
β-strand	359-361	3	17
α-helix	369-372	4
β-strand	374-378	5	18
β-strand	381-385	5	18
α-helix	387-389	3
β-strand	393-395	3	17
β-strand	413-417	5	17
β-strand	418-421	4	18
β-strand	423-424	2	16
α-helix	426-428	3
β-strand	433-435	3	16
α-helix	436-439	4
β-strand	441-456	16	17
β-strand	467-470	4	17
α-helix	476-482	7
α-helix	483-485	3
β-strand	486-491	6	12
β-strand	494-499	6	11

Chain D: 10 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	518-520	3
β-strand	529	1	19
α-helix	530-533	4
α-helix	534-536	3
α-helix	537-546	10
α-helix	549-552	4
α-helix	567-570	4
α-helix	573-595	23
β-strand	603-609	7	11
α-helix	619-624	6
β-strand	627	1	19
α-helix	628-635	8
α-helix	639-662	24

Chain E: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	42
β-strand	10-12	3	43
β-strand	18-25	8	42
α-helix	29-31	3
β-strand	34-39	6	43
α-helix	44	1
β-strand	45-51	7	43
β-strand	57-59	3	43
α-helix	61-63	3
β-strand	67-71A	6	42
β-strand	75-82	8	42
α-helix	84-86	3
β-strand	88-95	8	43
α-helix	96	1
β-strand	100E-103	4	43
β-strand	107-111	5	43
β-strand	118	1	44
α-helix	119-120	2
β-strand	121-125	5	45
β-strand	136-146	11	45
β-strand	147	1	44
α-helix	150	1
β-strand	151-155	5	46
α-helix	156-158	3
β-strand	160	1	46
β-strand	164-165	2	45
α-helix	167-169	3
β-strand	170-171	2	45
β-strand	177-186	10	45
β-strand	196-201	6	46
β-strand	206-211	6	46

Chain F: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	47
β-strand	10-13	4	48
β-strand	18-25	8	47
β-strand	33-38	6	48
β-strand	45-48	4	48
β-strand	54	1	48
α-helix	55	1
β-strand	62-63	2	47
β-strand	66	1	47
β-strand	70-76	7	47
β-strand	85-90	6	48
α-helix	96	1
β-strand	97-98	2	48
β-strand	102-106	5	48
β-strand	111	1	49
α-helix	112-113	2
β-strand	114-118	5	50
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	50
β-strand	140	1	49
β-strand	144-150	7	51
β-strand	153-155	3	51
β-strand	159-163	5	50
α-helix	164-166	3
β-strand	173-182	10	50
α-helix	183-188	6
β-strand	191-198	8	51
β-strand	206-210	5	51

Chain G: 14 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	20
β-strand	45-47	3	21
β-strand	53-56	4	22
α-helix	58-62	5
β-strand	68	1	23
β-strand	75-76	2	22
α-helix	77-78	2
β-strand	84-85	2	21
β-strand	91-94	4	24
α-helix	100-116	17
α-helix	120	1
β-strand	121	1	25
α-helix	123-125	3
β-strand	129-133	5	26
β-strand	154-162	9	26
β-strand	169-177	9	26
β-strand	181-183	3	26
β-strand	190-193	4	26
α-helix	194-197	4
β-strand	201-203	3	25
α-helix	204-205	2
β-strand	209	1	23
β-strand	215-218	4	22
α-helix	219-220	2
β-strand	223-228	6	21
β-strand	236-239	4	24
β-strand	242-245	4	21
β-strand	247	1	22
β-strand	251	1	22
β-strand	259-261	3	27
β-strand	271-273	3	27
β-strand	284-298	15	27
β-strand	301-312	10	28
β-strand	315-323	10	28
β-strand	330-334	5	27
α-helix	335-352	18
β-strand	360-361	2	27
α-helix	369-372	4
β-strand	374-378	5	29
β-strand	381-385	5	29
α-helix	387-389	3
β-strand	393-394	2	27
β-strand	413-417	5	27
β-strand	418-420	3	29
β-strand	423-424	2	25
α-helix	426-428	3
β-strand	433-435	3	25
α-helix	436-438	3
β-strand	443-456	14	27
β-strand	467-470	4	27
α-helix	476-482	7
β-strand	486-491	6	21
β-strand	494-499	6	20

Chain H: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	32
β-strand	10-12	3	33
β-strand	18-25	8	32
α-helix	29-31	3
β-strand	34-39	6	33
α-helix	44	1
β-strand	45-51	7	33
β-strand	57-59	3	33
α-helix	61-63	3
β-strand	67-71A	6	32
β-strand	75-82	8	32
α-helix	84-86	3
β-strand	88-95	8	33
α-helix	96	1
β-strand	100E-103	4	33
β-strand	107-111	5	33
β-strand	118	1	34
α-helix	119-120	2
β-strand	121-125	5	35
α-helix	130-133	4
β-strand	136-146	11	35
β-strand	147	1	34
α-helix	150	1
β-strand	151-155	5	36
α-helix	156-158	3
β-strand	160	1	36
β-strand	165	1	35
β-strand	170-171	2	35
β-strand	177-186	10	35
α-helix	187-189	3
β-strand	196-201	6	36
β-strand	206-211	6	36

4 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 gp120	A, C, G	protein	473	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp41	B, D, I	protein	153	Human immunodeficiency virus 1	Q2N0S7
VRC40.01 Fab Heavy chain	E, H, J	protein	229	Homo sapiens
VRC40.01 Fab Light chain	F, K, L	protein	214	Homo sapiens

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

>7LL1_1 Envelope glycoprotein gp120 (chains A, C, G)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSACTQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
MIRSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQCMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRV

Sequence of entity 2 (B, D, I), FASTA

>7LL1_2 Envelope glycoprotein gp41 (chains B, D, I)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAIEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 3 (E, H, J), FASTA

>7LL1_3 VRC40.01 Fab Heavy chain (chains E, H, J)
QVQLIQSGPQFKTPGASVTVSCKASGYIFTDYLIHWVRLVPGKGLEWLGRINTNAGLMYL
SHKFEGRLILRRVVDWRTPSLGTVNMELRNVRSDDSAIYFCGRVVDGFNAAGPLEFWGQG
SPVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTF
PAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 4 (F, K, L), FASTA

>7LL1_4 VRC40.01 Fab Light chain (chains F, K, L)
QVVMTQSPATLSLSPGETAAVSCRASQYVDRSISWYQLKTGRAPRLLVYAASSRSIGVPD
RFSGSGSGRDFTLTIRGVQSDDFALYYCQQDYYWPVTFGQGTRLDMKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Primary citation

Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies. Cottrell, C.A., Manne, K., Kong, R. et al. Cell Rep (2021) 37:109922-109922. DOI 10.1016/j.celrep.2021.109922 · 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…
6MTN 2.5 Å, Crystal Structure of HIV-1 BG505 SOSIP.664 Prefusion Env Trimer Bound to Small Molecule…
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

Browse structure collections

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