4WO4: Antigen-presenting glycoprotein CD1d

The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Nov 2014.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,806
Mol. weight: 96.15 kDa
Ligands: JLS
Released: 26 Nov 2014

Explore 4WO4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WO4 contains 35 α-helices and 74 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: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-20	11	1
β-strand	23-32	10	1
β-strand	35-40	6	1
β-strand	48-49	2	1
α-helix	60-88	29
α-helix	90-91	2
α-helix	93	1
β-strand	94-104	11	1
β-strand	110-118	9	1
β-strand	121-127	7	1
β-strand	130-133	4	1
α-helix	139-150	12
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
β-strand	188-194	7	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	236-237	2	3
β-strand	243-252	10	3
α-helix	254-256	3
β-strand	260-264	5	4
β-strand	273-276	4	4
α-helix	277-278	2

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	35-41	7	7
β-strand	44-45	2	7
α-helix	46	1
β-strand	49-51	3	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-84	7	7
β-strand	91-94	4	7

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	8
β-strand	10-14	5	9
β-strand	19-21	3	8
β-strand	24-26	3	8
β-strand	33-44	7	9
β-strand	50-57	8	9
α-helix	68-70	3
β-strand	71-72	2	8
β-strand	76-81	6	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-108	9	9
β-strand	111-114	4	9
β-strand	118-123	6	9
α-helix	124	1
β-strand	132-135	4	10
α-helix	136	1
β-strand	137	1	11
α-helix	138-139	2
β-strand	145-150	6	10
α-helix	156-161	6
β-strand	166-168	3	10
α-helix	169-171	3
β-strand	172-176	5	10
α-helix	177-179	3
β-strand	181-190	10	10
α-helix	197-200	4
α-helix	207-209	3
β-strand	211	1	10

Chain D: 12 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
α-helix	17-18	2
β-strand	19-25	7	12
β-strand	32-44	7	13
β-strand	50-57	8	13
α-helix	61-62	2
β-strand	66-67	2	13
β-strand	76-83	7	12
β-strand	86-91	6	12
α-helix	96-98	3
β-strand	100-108	9	13
β-strand	111-114	4	13
α-helix	115	1
β-strand	118-123	6	13
α-helix	126-128	3
β-strand	130	1	14
α-helix	131-132	2
β-strand	133-137	5	15
β-strand	138	1	11
α-helix	139-140	2
α-helix	141-147	7
β-strand	149-159	11	15
β-strand	160	1	14
β-strand	164-170	7	16
β-strand	173-175	3	16
β-strand	179-181	3	15
α-helix	185	1
β-strand	186-187	2	15
α-helix	195-196	2
β-strand	197-206	10	15
α-helix	207-210	4
β-strand	216-223	8	16
β-strand	226	1	17
α-helix	237-238	2
β-strand	240	1	17
β-strand	242-249	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A	protein	274	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
TCR variable DELTA 1 CHAIN and TCR constant Alpha	C	protein	207	Homo sapiens
TCR variable BETA 2 (TRVB20) chain and TCR constant BETA	D	protein	245	Homo sapiens

Sequence of entity 1 (A), FASTA

>4WO4_1 Antigen-presenting glycoprotein CD1d (chains A)
RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWET
LQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILS
FQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQV
KPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYL
RATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWPR

Sequence of entity 2 (B), FASTA

>4WO4_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>4WO4_3 TCR variable DELTA 1 CHAIN and TCR constant Alpha (chains C)
HMAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQNA
KSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGVTGKLTFGQGTILTVHPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 4 (D), FASTA

>4WO4_4 TCR variable BETA 2 (TRVB20) chain and TCR constant BETA (chains D)
HMGAVVSQHPSRVISKSGTSVKIECRSLDFQATTMFWYRQFPKQSLMLMATSNEGSKATY
EQGVEKDKFLINHASLTLSTLTVTSAHPEDSSFYICSAPGGVGAFFGQGTRLTVVEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Ligands and cofactors

ID	Name	Formula	Copies
JLS	(15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl…	C48 H93 N O9	1

Primary citation

The molecular bases of delta / alpha beta T cell-mediated antigen recognition. Pellicci, D.G., Uldrich, A.P., Le Nours, J. et al. J Exp Med (2014) 211:2599-2615. DOI 10.1084/jem.20141764 · PubMed

Other PDB entries of the same protein (UniProt P15813 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RSE 1.76 Å, Human CD1d with lipid antigen bound
8SOS 2.33 Å, Human CD1d presenting sphingomyelin C24:1 in complex with VHH nanobody 1D17
6V7Y 2.4 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D5
4WW2 2.48 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8,…
3HUJ 2.5 Å, Crystal structure of human CD1d-alpha-Galactosylceramide in complex with semi-invariant…
8SGM 2.5 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
4EN3 2.57 Å, Crystal structure of a human Valpha24(-) NKT TCR in complex with…
4MQ7 2.6 Å, Structure of human CD1d-sulfatide
6V7Z 2.75 Å, Human CD1d presenting alpha-Galactosylceramide in complex with VHH nanobody 1D22
3U0P 2.8 Å, Crystal structure of human CD1d-lysophosphatidylcholine
8SGB 2.8 Å, Crystal Structure of CD1d-lipid complexed with Beta-2-Microglobulin, TCR Alpha-Chain and…
9O4X 2.86 Å, Gamma delta T cell receptor bound to CD1d

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