4LHU: 9C2 TCR

Crystal Structure of 9C2 TCR bound to CD1d. Determined by X-ray diffraction at 2.87 Å resolution. Released 2 Oct 2013.

Method: X-ray diffraction
Resolution: 2.87 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,749
Mol. weight: 101.31 kDa
Ligands: NAG, BMA, MG, JLS
Released: 2 Oct 2013

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

Secondary structure: helices and β-sheets

4LHU contains 28 α-helices and 67 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: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	1
β-strand	24-32	9	1
β-strand	35-40	6	1
β-strand	47-49	3	1
α-helix	60-88	29
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	140-149	10
α-helix	152-159	8
α-helix	160-165	6
α-helix	166-176	11
α-helix	178-181	4
β-strand	188-192	5	2
α-helix	193-196	4
β-strand	202-211	10	2
β-strand	217-221	5	3
β-strand	226	1	3
α-helix	227	1
β-strand	231-232	2	2
β-strand	236-237	2	2
α-helix	238	1
β-strand	243-251	9	2
α-helix	254-256	3
β-strand	260-264	5	3
α-helix	272	1
β-strand	273-274	2	3

Chain B: 2 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	6-11	6	4
β-strand	21-30	10	4
β-strand	35-41	7	5
β-strand	44-45	2	5
α-helix	46	1
β-strand	50-51	2	4
α-helix	52-54	3
β-strand	55-56	2	4
β-strand	62-70	9	4
β-strand	78-84	7	5
β-strand	91-92	2	5

Chain D: 6 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	6
β-strand	13-17	5	7
β-strand	22-24	3	6
β-strand	27-29	3	6
β-strand	37-42	6	7
β-strand	48-53	6	7
α-helix	59-61	3
β-strand	62-63	2	6
β-strand	66-71	6	6
β-strand	76-81	6	6
α-helix	86-88	3
β-strand	91-97	7	7
β-strand	107-109	3	7
α-helix	110	1
β-strand	113-118	6	7
α-helix	119-121	3
α-helix	125-127	3
β-strand	128	1	8
β-strand	133-134	2	9
β-strand	137-138	2	9
β-strand	140-141	2	10
β-strand	143	1	8
β-strand	153-154	2	11
β-strand	159	1	12
α-helix	175-177	3
β-strand	178-179	2	10
β-strand	182	1	9
β-strand	183	1	12
β-strand	191-192	2	11

Chain G: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	13
β-strand	22-25	4	14
β-strand	35-41	7	13
α-helix	46-47	2
β-strand	48-54	7	13
β-strand	59-62	4	13
α-helix	63	1
α-helix	66-67	2
β-strand	71-74	4	14
β-strand	82-85	4	14
α-helix	90-92	3
β-strand	94-102	9	13
β-strand	112-115	4	13
β-strand	119-124	6	13
β-strand	135-138	4	15
α-helix	140-142	3
α-helix	143-148	6
β-strand	151-161	11	15
β-strand	167-168	2	16
β-strand	182-183	2	15
β-strand	187-189	3	15
β-strand	192-202	11	15
α-helix	203-205	3
β-strand	210-215	6	16
α-helix	224	1
β-strand	225-229	5	16
α-helix	230-232	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antigen-presenting glycoprotein CD1d	A	protein	278	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
9C2 TCR delta chain	D	protein	236	Homo sapiens	Q6PJ56 (AlphaFold model)
9C2 TCR gamma chain	G	protein	251	Homo sapiens	P0CF51 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4LHU_1 Antigen-presenting glycoprotein CD1d (chains A)
RLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFSDQQWET
LQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQGKDILS
FQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKSELKKQV
KPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNADETWYL
RATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 2 (B), FASTA

>4LHU_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (D), FASTA

>4LHU_3 9C2 TCR delta chain (chains D)
ETGAQKVTQAQSSVSMPVRKAVTLNCLYETSWWSYYIFWYKQLPSKEMIFLIRQGSDEQN
AKSGRYSVNFKKAAKSVALTISALQLEDSAKYFCALGDPGGLNTDKLIFGKGTRVTVEPR
SQPHTKPSVFVMKNGTNVACLVKEFYPKDIRINLVSSKKITEFDPAIVISPSGKYNAVKL
GKYEDSNSVTCSVQHDNKTVHSTDFEVKTDSTDHVKPKETENTKQPSKSASGLVPR

Sequence of entity 4 (G), FASTA

>4LHU_4 9C2 TCR gamma chain (chains G)
ETGSSNLEGGTKSVTRPTRSSAEITCDLTVINAFYIHWYLHQEGKAPQRLLYYDVSNSKD
VLESGLSPGKYYTHTPRRWSWILILRNLIENDSGVYYCATWDRGNPKTHYYKKLFGSGTT
LVVTDKQLDADVSPKPTIFLPSIAETKLQKAGTYLCLLEKFFPDVIKIHWQEKKSNTILG
SQEGNTMKTNDTYMKFSWLTVPEESLDKEHRCIVRHENNKNGVDQEIIFPPIKTDVITMD
PKDNASGLVPR

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
BMA	beta-D-mannopyranose	C6 H12 O6	1
MG	Magnesium ion	Mg	1
JLS	(15Z)-N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl…	C48 H93 N O9	1

Water and common crystallization additives (CL) are not listed.

Primary citation

CD1d-lipid antigen recognition by the gamma delta TCR. Uldrich, A.P., Le Nours, J., Pellicci, D.G. et al. Nat Immunol (2013) 14:1137-1145. DOI 10.1038/ni.2713 · 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…
4WO4 2.5 Å, The molecular bases of Delta/Alpha beta T cell-mediated antigen recognition.
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…

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