7LY9: 2909 Fab

Cryo-EM structure of 2909 Fab in complex with 3BNC117 Fab and CAP256.wk34.c80 SOSIP.RnS2 N160K HIV-1 Env trimer. Determined by electron microscopy at 3.91 Å resolution. Released 18 Aug 2021.

Method: Electron microscopy
Resolution: 3.91 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 14
Atoms: 21,464
Mol. weight: 422.72 kDa
Ligands: NAG
Released: 18 Aug 2021

Explore 7LY9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LY9 contains 60 α-helices and 241 β-strands across 14 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	66
β-strand	10-11	2	67
β-strand	18-24	7	66
α-helix	29-31	3
β-strand	34-39	6	67
β-strand	45-51	7	67
β-strand	57-58	2	67
β-strand	67-71A	6	66
β-strand	76-82	7	66
α-helix	84-86	3
β-strand	88-95	8	67
β-strand	100B-103	4	67
β-strand	107-110	4	67

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	22
α-helix	7-9	3
β-strand	18-24	7	22
α-helix	29-31	3
β-strand	33-39	7	23
β-strand	46-51	6	23
β-strand	57-58	2	23
β-strand	68-71A	5	22
β-strand	76-82	7	22
β-strand	88-95	8	23
β-strand	96	1	24
β-strand	99	1	24
β-strand	107-109	3	23

Chain C: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	25
β-strand	19-20	2	26
β-strand	23-25	3	25
β-strand	34-38	5	27
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	63	1	26
β-strand	66-67	2	25
β-strand	70-71	2	25
β-strand	74-75	2	26
β-strand	85-89	5	27
β-strand	98	1	27
β-strand	102	1	27

Chain D: 8 helices, 49 β-strands

Element	Residues	Length	Sheet
β-strand	36-40	5	28
β-strand	45-47	3	29
β-strand	53	1	30
β-strand	55-56	2	31
β-strand	67	1	32
α-helix	71-73	3
β-strand	75-76	2	31
α-helix	77-78	2
β-strand	84-85	2	29
β-strand	91-94	4	33
α-helix	99-116	18
β-strand	121	1	34
β-strand	129	1	35
β-strand	130-131	2	36
β-strand	154-161	8	36
β-strand	170-177	8	36
β-strand	181-183	3	35
β-strand	191-193	3	35
β-strand	202	1	34
β-strand	203	1	37
α-helix	204-205	2
β-strand	209	1	32
β-strand	215	1	38
β-strand	218	1	30
α-helix	219-220	2
β-strand	223-228	6	29
β-strand	236-239	4	33
β-strand	242-245	4	29
β-strand	247	1	30
β-strand	251	1	38
β-strand	259-261	3	39
β-strand	271-274	4	40
β-strand	284-287	4	40
β-strand	292-293	2	39
β-strand	294-297	4	41
β-strand	301	1	42
β-strand	305-312	6	43
β-strand	315-319	5	43
β-strand	323	1	42
β-strand	330-334	5	41
α-helix	335-353	19
β-strand	359-361	3	40
β-strand	374-378	5	44
β-strand	381-385	5	44
β-strand	394-395	2	40
β-strand	413-417	5	41
β-strand	418-420	3	44
β-strand	423	1	37
β-strand	435	1	37
α-helix	436-438	3
β-strand	444-445	2	41
β-strand	448-452	5	39
β-strand	453-456	4	40
β-strand	466-470	5	40
α-helix	476-480	5
β-strand	488-491	4	29
β-strand	494-498	5	28

Chain E: 1 helix, 10 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	45
β-strand	10-11	2	46
β-strand	18-24	7	45
β-strand	34-39	6	46
β-strand	46-51	6	46
β-strand	57-58	2	46
β-strand	67-71A	6	45
β-strand	76-82	7	45
α-helix	84-86	3
β-strand	88-92	5	46
β-strand	107-110	4	46

Chain F: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	517-523	7
α-helix	530-535	6
α-helix	570-595	26
β-strand	603	1	9
β-strand	609	1	9
α-helix	619-625	7
α-helix	628-636	9
α-helix	639-656	18

Chain G: 9 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	9
β-strand	45-47	3	10
β-strand	53-56	4	11
β-strand	67	1	12
β-strand	75-76	2	11
α-helix	77-78	2
β-strand	85	1	10
β-strand	91-92	2	13
α-helix	95-97	3
α-helix	100-115	16
β-strand	121	1	14
β-strand	129-131	3	15
β-strand	154-162	9	15
β-strand	169-177	9	15
α-helix	178-180	3
β-strand	181-183	3	15
β-strand	190-193	4	15
β-strand	200-203	4	14
α-helix	204-205	2
β-strand	209	1	12
β-strand	215	1	16
β-strand	216-218	3	11
β-strand	223-228	6	10
β-strand	238-239	2	13
β-strand	242-245	4	10
β-strand	247	1	11
β-strand	251	1	16
β-strand	259-261	3	17
β-strand	271-274	4	18
β-strand	284-287	4	18
β-strand	292-297	6	17
β-strand	301	1	19
β-strand	304-312	7	15
β-strand	315-320	6	15
β-strand	323	1	19
β-strand	332-334	3	17
α-helix	335-353	19
β-strand	358	1	20
β-strand	361	1	18
α-helix	369-372	4
β-strand	374-378	5	21
β-strand	381-385	5	21
α-helix	389-391	3
β-strand	413-415	3	17
β-strand	418-420	3	21
β-strand	423-424	2	14
β-strand	432-435	4	14
β-strand	444-452	9	17
β-strand	453-456	4	18
β-strand	465	1	20
β-strand	468-470	3	18
α-helix	477-480	4
β-strand	488-491	4	10
β-strand	494-499	6	9

Chain H: 1 helix, 15 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	4
β-strand	11	1	5
β-strand	17-18	2	6
β-strand	21-25	5	4
β-strand	34-39	6	7
β-strand	45-50	6	7
β-strand	59	1	7
α-helix	61-63	3
β-strand	69-72	4	4
β-strand	77-80	4	4
β-strand	82-82A	2	6
β-strand	89-95	7	7
β-strand	99-100	2	8
β-strand	100H-100I	2	8
β-strand	100M-103	4	7
β-strand	110	1	5

6 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
2909 Light Chain	L	protein	211	Homo sapiens
2909 Heavy Chain	H	protein	231	Homo sapiens
Envelope glycoprotein gp120	D, G, K	protein	471	Human immunodeficiency virus 1	A0A0N9FF17
3BNC117 Heavy Chain	A, B, E	protein	226	Homo sapiens
3BNC117 Light Chain	C, I, M	protein	206	Homo sapiens
Envelope glycoprotein gp41	F, J, N	protein	154	Human immunodeficiency virus 1	W6HZ60

Sequence of entity 1 (L), FASTA

>7LY9_1 2909 Light Chain (chains L)
SYVLTQPPSVSVAPGKTARITCGGNNIANKNVHWYQQKPGQAPVLVIYYDDDRPSGIPDR
FSGSNSGNTATLTISRVEAGDEADYYCQVWDSNSDHVVFGGGTQLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT

Sequence of entity 2 (H), FASTA

>7LY9_2 2909 Heavy Chain (chains H)
EVQLVESGGNVVQPGGSLRLSCTASGFSFDDSTMHWVRQAPGKGLQWVSLISWNGGRTYY
ADSVKGRFTISRDNSKNSLYLQMNSLKTEDTAFYFCAKDKGDSDYDYNLGYSYFYYMDGW
GKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGV
HTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Sequence of entity 3 (D, G, K), FASTA

>7LY9_3 Envelope glycoprotein gp120 (chains D, G, K)
GLWVTVYYGVPVWREAKTTLFCASDAKSYEKEVHNVWATHACVPTDPNPQELVLENVTEN
FNMWKNDMVDQMHEDIISLWDQSLKPCVKLTPLCVTLNCSDAKVNATYKGTREEIKNCSF
KATTELRDKKRREYALFYRLDIVPLSGEGNNNSEYRLINCNTSVITQICPKVTFDPIPIH
YCAPAGYAILKCNNKTFNGTGPCNNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSEN
LTDNVKTIIVHLNESVEITCTRPNNMTRKSVRIGPGQTFYALGDIIGDIRQPHCNISEIK
WEKTLQRVSEKLREHFNKTIIFNQSSGGDLEITTHSFNCGGEFFYCNTSDLFFNKTFNET
YSTGSNSTNSTITLPCRIKQIINMWQEVGRAMYAPPIAGNITCKSNITGLLLTRDGGGNN
STKETFRPGGGNMRDNWRSELYKYKVVEVKPLGIAPTECNRTVVQRRRRRR

Sequence of entity 4 (A, B, E), FASTA

>7LY9_4 3BNC117 Heavy Chain (chains A, B, E)
QVQLLQSGAAVTKPGASVRVSCEASGYNIRDYFIHWWRQAPGQGLQWVGWINPKTGQPNN
PRQFQGRVSLTRHASWDFDTYSFYMDLKALRSDDTAVYFCARQRSDYWDFDVWGSGTQVT
VSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVL
QSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Sequence of entity 5 (C, I, M), FASTA

>7LY9_5 3BNC117 Light Chain (chains C, I, M)
DIQMTQSPSSLSASVGDTVTITCQANGYLNWYQQRRGKAPKLLIYDGSKLERGVPSRFSG
RRWGQEYNLTINNLQPEDIATYFCQVYEFVVPGTRLDLKRTVAAPSVFIFPPSDEQLKSG
TASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEK
HKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (F, J, N), FASTA

>7LY9_6 Envelope glycoprotein gp41 (chains F, J, N)
AVVGLGAVFLGFLGAAGSTMGAASNTLTVQARQLLSGIVQQQSNLLRAPEAQQHMLQLGV
WGFKQLQARVLAIERYLEVQQLLGMWGCSGKLICCTNVPWNSSWSNKTYNEIWDNMTWMQ
WDREIGNYTDTIYKLLEVSQFQQEINEKDNLTLD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	54

Primary citation

Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces. Lee, M., Changela, A., Gorman, J. et al. Nat Commun (2021) 12:6470-6470. DOI 10.1038/s41467-021-26579-z · PubMed

Other PDB entries of the same protein (UniProt A0A0N9FF17), best resolution first:

6VZI 2.72 Å, Crystal Structure of HIV-1 CAP256 RnS-3mut-2G-SOSIP.664 Prefusion Env Trimer in Complex…
6VTT 3.7 Å, Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80…
6VRW 3.71 Å, Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
9BTH 4.2 Å, Rhesus Fab 42056-a.01 in complex with CAP256SU.wk34 RnS SOSIP Env

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