5WKI: PG90 TCR-CD1b-PG complex

Crystal structure of PG90 TCR-CD1b-PG complex. Determined by X-ray diffraction at 2.75 Å resolution. Released 1 Nov 2017.

Method: X-ray diffraction
Resolution: 2.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,732
Mol. weight: 99.16 kDa
Ligands: NAG, CUY, D3D
Released: 1 Nov 2017

Explore 5WKI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WKI contains 20 α-helices and 70 β-strands across 4 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: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-20	12	1
β-strand	23-32	10	1
β-strand	35-41	7	1
β-strand	46-49	4	1
α-helix	60-83	24
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-126	6	1
β-strand	131-133	3	1
α-helix	139-148	10
α-helix	152-160	9
α-helix	161-165	5
α-helix	166-176	11
α-helix	178-181	4
β-strand	185	1	2
α-helix	186-187	2
β-strand	188-193	6	3
β-strand	201-211	11	3
β-strand	212	1	2
β-strand	217-222	6	4
β-strand	225-226	2	4
β-strand	231-232	2	3
β-strand	236-238	3	3
β-strand	242-252	11	3
β-strand	260-264	5	4
α-helix	266-268	3
β-strand	273-276	4	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
β-strand	9-13	5	6
β-strand	23-32	10	6
β-strand	33	1	5
β-strand	38-43	6	7
β-strand	46-47	2	7
α-helix	48	1
β-strand	52-53	2	6
α-helix	54-56	3
β-strand	57-58	2	6
β-strand	64-72	9	6
β-strand	80-85	6	7
β-strand	93-96	4	7

Chain D: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	9-13	5	9
β-strand	18-23	6	8
β-strand	31-38	8	9
β-strand	45-50	6	9
α-helix	54	1
β-strand	55-56	2	8
β-strand	61-64	4	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-92	9	9
β-strand	104-109	6	9
β-strand	118-124	7	10
β-strand	131-136	6	10
β-strand	152-154	3	10
α-helix	155-157	3
β-strand	158-162	5	10
β-strand	167-176	10	10
β-strand	197	1	10

Chain E: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-24	6	11
β-strand	31-37	7	12
β-strand	44-50	7	12
β-strand	53-56	4	12
β-strand	65-68	4	11
β-strand	75-79	5	11
α-helix	84-86	3
β-strand	88-95	8	12
β-strand	109-110	2	12
β-strand	114-119	6	12
α-helix	122-124	3
β-strand	126	1	13
β-strand	129-134	6	10
α-helix	135-136	2
α-helix	137-143	7
β-strand	145-155	11	10
β-strand	156	1	13
β-strand	160-166	7	14
β-strand	169-171	3	14
β-strand	175-177	3	10
α-helix	181	1
β-strand	182-183	2	10
β-strand	193-202	10	10
α-helix	203-206	4
β-strand	212-219	8	14
β-strand	222	1	15
α-helix	233-234	2
β-strand	236	1	15
β-strand	238-245	8	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-cell surface glycoprotein CD1b	A	protein	300	Homo sapiens	P29016 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
T-cell receptor alpha variable 26-1,TRA@ protein	D	protein	204	Homo sapiens	A0A087WT03 (AlphaFold model), Q6P4G7 (AlphaFold model)
PG90 TCR beta chain	E	protein	249	Homo sapiens

Sequence of entity 1 (A), FASTA

>5WKI_1 T-cell surface glycoprotein CD1b (chains A)
HAFQGPTSFHVIQTSSFTNSTWAQTQGSGWLDDLQIHGWDSDSGTAIFLKPWSKGNFSDK
EVAELEEIFRVYIFGFAREVQDFAGDFQMKYPFEIQGIAGCELHSGGAIVSFLRGALGGL
DFLSVKNASCVPSPEGGSRAQKFCALIIQYQGIMETVRILLYETCPRYLLGVLNAGKADL
QRQVKPEAWLSSGPSPGPGRLQLVCHVSGFYPKPVWVMWMRGEQEQQGTQLGDILPNANW
TWYLRATLDVADGEAAGLSCRVKHSSLEGQDIILYWRGSGLNDIFEAQKIEWHEHHHHHH

Sequence of entity 2 (B), FASTA

>5WKI_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>5WKI_3 T-cell receptor alpha variable 26-1,TRA@ protein (chains D)
DAKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMA
SLIITEDRKSSTLILPHATLRDTAVYYCIVRVAYRQKVTFGTGTKLQVIPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (E), FASTA

>5WKI_4 PG90 TCR beta chain (chains E)
GAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSGL
PSDRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSLARAQGASNTGELFFGEGSRLTVLE
DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQ
PLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIV
SAEAWGRAD

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
CUY	tetracosyl octadecanoate	C42 H84 O2	1
D3D	(19S,22R,25R)-22,25,26-trihydroxy-16,22-dioxo-17,21,23-trioxa-22lambda~5~-phosp…	C40 H77 O10 P	1

Water and common crystallization additives (NA, EDO, CL, ACT) are not listed.

Primary citation

A molecular basis of human T cell receptor autoreactivity toward self-phospholipids. Shahine, A., Van Rhijn, I., Cheng, T.Y. et al. Sci Immunol (2017) 2. DOI 10.1126/sciimmunol.aao1384 · PubMed

Other PDB entries of the same protein (UniProt P29016 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WL1 1.38 Å, Crystal Structure of Human CD1b in Complex with PG
8GLG 1.6 Å, Crystal Structure of Human CD1b in Complex with Phosphatidylethanolamine C34:1
5L2J 1.65 Å, Crystal Structure of human CD1b in complex with C36-GMM
5WKE 1.69 Å, Crystal Structure of Human CD1b in Complex with PS
6D64 1.7 Å, Crystal Structure of Human CD1b in Complex with POPC
7MX4 1.73 Å, CD1c with antigen analogue 1
2H26 1.8 Å, human CD1b in complex with endogenous phosphatidylcholine and spacer
8GLH 1.83 Å, Crystal Structure of Human CD1b in Complex with Endogenous PC C40:5
9OI0 1.84 Å, Crystal structure of CD1b presenting ganglioside GD3
8GLE 1.85 Å, Crystal Structure of Human CD1b in Complex with Lysosulfatide
3T8X 1.9 Å, Crystal structure of human CD1b in complex with synthetic antigenic…
8DV3 1.9 Å, Crystal structure of human CD1b presenting Phosphatidylinositol C34:1

Browse structure collections

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