6UDK: HIV-1 bNAb 1-55

HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074. Determined by electron microscopy at 3.9 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 18
Atoms: 25,724
Mol. weight: 540.02 kDa
Ligands: NAG
Released: 29 Jan 2020

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

Secondary structure: helices and β-sheets

6UDK contains 44 α-helices and 283 β-strands across 18 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: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	42
β-strand	11-12	2	43
β-strand	18	1	42
β-strand	21-25	5	42
β-strand	35-39	5	44
β-strand	45-50	6	44
β-strand	59	1	44
β-strand	67-72	6	42
β-strand	77-82	6	42
β-strand	88-93	6	44
β-strand	96-100A	6	45
β-strand	100J-100O	6	45
β-strand	108-109	2	44
β-strand	110-111	2	43

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	46
β-strand	20-21	2	47
α-helix	26-27	2
β-strand	34-38	5	46
β-strand	45-49	5	46
β-strand	53	1	46
β-strand	62-63	2	47
β-strand	73-75	3	47
β-strand	85-89	5	46
β-strand	102-104	3	46

Chain C: 6 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	538-541	4
α-helix	571-592	22
β-strand	603-609	7	1
α-helix	610-611	2
α-helix	619-622	4
α-helix	628-632	5
α-helix	639-661	23

Chain D: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	69
β-strand	18-19	2	70
β-strand	22	1	71
β-strand	35D-39	7	72
β-strand	46-47	2	72
β-strand	50-51	2	72
β-strand	57-58	2	72
β-strand	67-68	2	70
β-strand	78	1	71
β-strand	81-82	2	70
β-strand	88-95	8	72
β-strand	103-109	7	72
β-strand	110-111	2	69

Chain E: 0 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	73
β-strand	10	1	74
β-strand	13	1	75
β-strand	19-25	7	73
β-strand	33-37	5	74
β-strand	45-48	4	74
β-strand	62-63	2	73
β-strand	66-67	2	73
β-strand	70-75	6	73
β-strand	85-90	6	74
β-strand	98	1	74
β-strand	102-103	2	74
β-strand	106	1	75

Chain F: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	48
β-strand	11-12	2	49
β-strand	19	1	50
β-strand	21-25	5	48
β-strand	35-39	5	51
β-strand	45-50	6	51
β-strand	58-59	2	51
β-strand	67-72	6	50
β-strand	77-82	6	50
β-strand	88-93	6	51
β-strand	96-100A	6	52
β-strand	100J-100O	6	52
β-strand	108-109	2	51
β-strand	110-111	2	49

Chain G: 7 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	45-46	2	2
β-strand	53-55	3	3
β-strand	75	1	3
β-strand	84-85	2	2
β-strand	91-93	3	4
α-helix	104-114	11
β-strand	120-121	2	5
β-strand	129-133	5	6
β-strand	155-162	8	6
β-strand	169-176	8	6
β-strand	181-183	3	6
β-strand	189-193	5	6
β-strand	201-203	3	5
α-helix	204-205	2
β-strand	215	1	7
β-strand	216-218	3	3
β-strand	223-228	6	2
β-strand	237-239	3	4
β-strand	242-245	4	2
β-strand	247	1	3
β-strand	251	1	7
β-strand	259	1	8
β-strand	271-273	3	9
β-strand	284-287	4	9
β-strand	292-298	7	10
β-strand	304-307	4	11
β-strand	317-320	4	11
β-strand	330-334	5	10
α-helix	335-349	15
β-strand	359	1	12
β-strand	361	1	9
α-helix	369-372	4
β-strand	374-379	6	13
β-strand	381-385	5	13
α-helix	388-390	3
β-strand	395	1	12
β-strand	413-417	5	10
β-strand	418-420	3	13
β-strand	424	1	5
α-helix	426-428	3
β-strand	433-435	3	5
β-strand	443-449	7	10
β-strand	452	1	8
β-strand	453-456	4	9
β-strand	468-470	3	9
α-helix	475-477	3
β-strand	486-491	6	2
β-strand	494-499	6	1

Chain H: 0 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	76
β-strand	11-12	2	77
β-strand	18-19	2	78
β-strand	22-24	3	76
β-strand	35D-39	7	79
β-strand	46-51	6	79
β-strand	57-58	2	79
β-strand	68	1	78
β-strand	71	1	76
β-strand	78	1	76
β-strand	81-82	2	78
β-strand	88-95	8	79
β-strand	102-109	8	79
β-strand	110-111	2	77

10 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
RC1 variant of HIV-1 Env glycoprotein gp120	G, K, R	protein	481	Human immunodeficiency virus 1	Q2N0S6
10-1074 Fab Heavy Chain	A, F, O	protein	238	Homo sapiens	S6B2B6 (AlphaFold model)
10-1074 Fab Light Chain	B, I, P	protein	214	Homo sapiens	Q8N355 (AlphaFold model)
1-55 Fab Heavy Chain	D, H, M	protein	262	Homo sapiens	S6C4S0 (AlphaFold model)
1-55 Fab Light Chain	E, L, N	protein	234	Homo sapiens	Q6PJF2
RC1 variant of HIV-1 Env glycoprotein gp41	C, J, Q	protein	153	Human immunodeficiency virus 1	Q2N0S6

Sequence of entity 1 (G, K, R), FASTA

>6UDK_1 RC1 variant of HIV-1 Env glycoprotein gp120 (chains G, K, R)
AENLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVT
EEFNMWKNNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLQCTNYAPNLLSNMRGELKQCS
FNMTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSF
EPIPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEV
IIRSENITNNAKNILVQLNTPVQINCTRPNNNTVKSIRIGPGQAFYYFGDIIGDIRMAHC
NVSKATWNETLGKVVKQLRKHFGNNTIIRFAQSSGGDLEVTTHSFNCGGEFFYCNTSGLF
NSTWISNTSVQGSNSTGSNDSIVLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGL
ILTRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRR
R

Sequence of entity 2 (A, F, O), FASTA

>6UDK_2 10-1074 Fab Heavy Chain (chains A, F, O)
QVQLQESGPGLVKPSETLSVTCSVSGDSMNNYYWTWIRQSPGKGLEWIGYISDRESATYN
PSLNSRVVISRDTSKNQLSLKLNSVTPADTAVYYCATARRGQRIYGVVSFGEFFYYYSMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKT

Sequence of entity 3 (B, I, P), FASTA

>6UDK_3 10-1074 Fab Light Chain (chains B, I, P)
SYVRPLSVALGETARISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGT
PDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Sequence of entity 4 (D, H, M), FASTA

>6UDK_4 1-55 Fab Heavy Chain (chains D, H, M)
MGWSCIILFLVATATGAHSQGRLFQSGTEVKRPGASVKISCRADDDPYTDDDTFTKYYTH
WIRQAPGQPPEWLGVISPHFARPIYSYKFRDRLTLTRDSSLTAVYFELRGLQPDDTGIYF
CARDPFGDMYPHYNYHMDVWGGGTTVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPS
NTKVDKRVEPKSCDKTHHHHHH

Sequence of entity 5 (E, L, N), FASTA

>6UDK_5 1-55 Fab Light Chain (chains E, L, N)
MGWSCIILFLVATATGVHSEIVLTQSPAILSVSPGDRVILSCKASEGLSSSDLAWYRFKG
GQIPTLVIFGASNRARGTPDRFSGSGSGTDFTLTINRVEPEDFATYYCQRYGGTPITFGG
GTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 6 (C, J, Q), FASTA

>6UDK_6 RC1 variant of HIV-1 Env glycoprotein gp41 (chains C, J, Q)
AVGIGAVSLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEPQQHLLKDTHW
GIKQLQARVLAVEHYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	27

Primary citation

Restriction of HIV-1 Escape by a Highly Broad and Potent Neutralizing Antibody. Schommers, P., Gruell, H., Abernathy, M.E. et al. Cell (2020) 180:471. DOI 10.1016/j.cell.2020.01.010 · 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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