6UDJ: HIV-1 bNAb 1-18

HIV-1 bNAb 1-18 in complex with BG505 SOSIP.664 and 10-1074. Determined by electron microscopy at 2.5 Å resolution. Released 29 Jan 2020.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Homo sapiens, Human immunodeficiency virus 1
Chains: 18
Atoms: 26,592
Mol. weight: 629.04 kDa
Ligands: NAG
Released: 29 Jan 2020

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

Secondary structure: helices and β-sheets

6UDJ contains 83 α-helices and 248 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.

Chains A and K: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
β-strand	33-39	7	3
β-strand	45-51	7	3
β-strand	58-59	2	3
α-helix	61-63	3
β-strand	67-72	6	1
β-strand	77-82	6	1
α-helix	84-86	3
β-strand	88-100A	14	3
α-helix	100E-100G	3
β-strand	100J-102	9	3
β-strand	107-109	3	3
β-strand	110-111	2	2

Chain B: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	16
β-strand	18-22	5	17
α-helix	23	1
β-strand	31-38	8	16
α-helix	43-44	2
β-strand	45-48	4	16
β-strand	49	1	18
β-strand	53	1	18
α-helix	54-55	2
β-strand	62-64	3	17
β-strand	72-76	5	17
β-strand	85-92	8	16
β-strand	102-107	6	16

Chain C: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	530-533	4
α-helix	537-541	5
α-helix	570-595	26
β-strand	603-609	7	30
α-helix	619-623	5
α-helix	628-634	7
α-helix	636-638	3
α-helix	639-660	22

Chain D: 3 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	19
α-helix	7-9	3
β-strand	10-12	3	20
β-strand	18-23	6	19
α-helix	34-35B	4
β-strand	35D-39	7	20
β-strand	46-51	6	20
β-strand	57-59	3	20
β-strand	67-71	5	19
β-strand	77-82	6	19
α-helix	84-86	3
β-strand	88-95	8	20
β-strand	102-111	10	20

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	10
β-strand	10-13	4	11
β-strand	19-25	7	10
β-strand	33-38	6	11
β-strand	45-49	5	11
β-strand	53-54	2	11
β-strand	62-67	6	10
β-strand	70-75	6	10
α-helix	80-82	3
β-strand	85-90	6	11
α-helix	96	1
β-strand	97-98	2	11
β-strand	102-106	5	11

Chain F: 7 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	524-526	3
α-helix	530-533	4
α-helix	537-541	5
α-helix	570-594	25
β-strand	603-609	7	49
α-helix	619-623	5
α-helix	628-635	8
α-helix	639-660	22

Chain G: 10 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	30
β-strand	45-47	3	31
β-strand	53-55	3	32
β-strand	67	1	33
α-helix	71-73	3
β-strand	75	1	32
β-strand	84-86	3	31
β-strand	91-94	4	34
α-helix	99-114	16
β-strand	121	1	35
β-strand	129-133	5	36
β-strand	154-162	9	36
β-strand	169-177	9	36
α-helix	178-180	3
β-strand	181-183	3	36
β-strand	189-193	5	36
β-strand	200-203	4	35
α-helix	204-205	2
β-strand	209	1	33
β-strand	215	1	37
β-strand	216-218	3	32
β-strand	223-228	6	31
β-strand	236-239	4	34
β-strand	242-245	4	31
β-strand	247	1	32
β-strand	251	1	37
β-strand	256	1	38
β-strand	259-261	3	38
α-helix	264-266	3
β-strand	271-274	4	38
β-strand	284-312	27	38
β-strand	315-323	10	38
β-strand	329-334	6	38
α-helix	335-349	15
β-strand	358-361	4	38
α-helix	369-372	4
β-strand	374-378	5	38
β-strand	381-385	5	38
β-strand	393-395	3	38
β-strand	413-421	9	38
β-strand	423-424	2	35
β-strand	432-435	4	35
α-helix	436-439	4
β-strand	441-456	16	38
α-helix	457-459	3
β-strand	465-470	6	38
α-helix	476-480	5
β-strand	486-491	6	31
β-strand	494-499	6	30

Chain H: 2 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	28
α-helix	7-9	3
β-strand	10-12	3	29
β-strand	18-23	6	28
β-strand	35D-39	7	29
β-strand	46-51	6	29
β-strand	57-59	3	29
β-strand	67-71	5	28
β-strand	77-82	6	28
α-helix	84-86	3
β-strand	88-95	8	29
β-strand	102-111	10	29

9 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
10-1074 Fab Heavy Chain	A, K, Q	protein	238	Homo sapiens	S6B2B6 (AlphaFold model)
1-18 Fab Light Chain	E, I, O	protein	234	Homo sapiens	Q6PIL8 (AlphaFold model)
10-1074 Fab Light Chain	B, L, R	protein	214	Homo sapiens	Q8N355 (AlphaFold model)
1-18 Fab Heavy Chain	D, H, N	protein	480	Homo sapiens
Envelope glycoprotein gp41	C, F, M	protein	153	Human immunodeficiency virus 1	Q2N0S6
Envelope glycoprotein gp120	G, J, P	protein	479	Human immunodeficiency virus 1	Q2N0S6

Sequence of entity 1 (A, K, Q), FASTA

>6UDJ_1 10-1074 Fab Heavy Chain (chains A, K, Q)
QVQLQESGPGLVKPSETLSVTCSVSGDSMNNYYWTWIRQSPGKGLEWIGYISDRESATYN
PSLNSRVVISRDTSKNQLSLKLNSVTPADTAVYYCATARRGQRIYGVVSFGEFFYYYSMD
VWGKGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTS
GVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKT

Sequence of entity 2 (E, I, O), FASTA

>6UDJ_2 1-18 Fab Light Chain (chains E, I, O)
MGWSCIILFLVATATGVAGEVVLTQSPAILSVSPGDRVILSCRASQGLDSSHLAWYRFKR
GQIPTLVIFGTSNRARGTPDRFSGSGSGADFTLTISRVEPEDFATYYCQRYGGTPITFGG
GTTLDKKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ
ESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (B, L, R), FASTA

>6UDJ_3 10-1074 Fab Light Chain (chains B, L, R)
SYVRPLSVALGETARISCGRQALGSRAVQWYQHRPGQAPILLIYNNQDRPSGIPERFSGT
PDINFGTRATLTISGVEAGDEADYYCHMWDSRSGFSWSFGGATRLTVLGQPKAAPSVTLF
PPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYL
SLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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

>6UDJ_4 1-18 Fab Heavy Chain (chains D, H, N)
MGWSCIILFLVATATGAHSQGRLFQSGAEVKRPGASVRISCRADDDPYTDDDTFTKYWTH
WIRQAPGQRPEWLGVISPHFARPIYSYKFRDRLTLTRDSSLTAVYLELKGLQPDDSGIYF
CARDPFGDRAPHYNYHMDVWGGGTAVIVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPS
NTKVDKRVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVS
HEDPEVKFNWYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKA
LPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQP
ENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

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

>6UDJ_5 Envelope glycoprotein gp41 (chains C, F, M)
AVGIGAVFLGFLGAAGSTMGAASMTLTVQARNLLSGIVQQQSNLLRAPEAQQHLLKLTVW
GIKQLQARVLAVERYLRDQQLLGIWGCSGKLICCTNVPWNSSWSNRNLSEIWDNMTWLQW
DKEISNYTQIIYGLLEESQNQQEKNEQDLLALD

Sequence of entity 6 (G, J, P), FASTA

>6UDJ_6 Envelope glycoprotein gp120 (chains G, J, P)
NLWVTVYYGVPVWKDAETTLFCASDAKAYETEKHNVWATHACVPTDPNPQEIHLENVTEE
FNMWKNNMVEQMHTDIISLWDQSLKPCVKLTPLCVTLQCTNVTNNITDDMRGELKNCSFN
MTTELRDKKQKVYSLFYRLDVVQINENQGNRSNNSNKEYRLINCNTSAITQACPKVSFEP
IPIHYCAPAGFAILKCKDKKFNGTGPCPSVSTVQCTHGIKPVVSTQLLLNGSLAEEEVMI
RSENITNNAKNILVQFNTPVQINCTRPNNNTRKSIRIGPGQAFYATGDIIGDIRQAHCNV
SKATWNETLGKVVKQLRKHFGNNTIIRFANSSGGDLEVTTHSFNCGGEFFYCNTSGLFNS
TWISNTSVQGSNSTGSNDSITLPCRIKQIINMWQRIGQAMYAPPIQGVIRCVSNITGLIL
TRDGGSTNSTTETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTRCKRRVVGRRRRRR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	15

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 S6B2B6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W6C 1.63 Å, UCA Fab (unbound) from 6649 Lineage
5W6G 2.79 Å, Human antibody 6649 in complex with influenza hemagglutinin H1 Solomon Islands
6UDK 3.9 Å, HIV-1 bNAb 1-55 in complex with modified BG505 SOSIP-based immunogen RC1 and 10-1074
5W1K 3.99 Å, JUNV GP1 CR1-10 Fab CR1-28 Fab complex

Browse structure collections

About this viewer

MolViewer shows 6UDJ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.