4WWK: TCR Alpha Chain-TRAV12-3

Crystal structure of human TCR Alpha Chain-TRAV12-3, Beta Chain-TRBV6-5, Antigen-presenting molecule CD1d, and Beta-2-microglobulin. Determined by X-ray diffraction at 3.1 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,883
Mol. weight: 96.99 kDa
Ligands: JLS, NAG
Released: 3 Feb 2016

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

Secondary structure: helices and β-sheets

4WWK contains 27 α-helices and 76 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: 5 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	11-14	4	1
β-strand	19-24	6	2
β-strand	32-44	7	1
β-strand	51-56	6	1
β-strand	60	1	2
β-strand	67-68	2	2
β-strand	76-81	6	2
β-strand	86-91	6	2
α-helix	96-98	3
β-strand	100-107	8	1
α-helix	113-115	3
β-strand	118-119	2	1
β-strand	123-128	6	1
β-strand	139	1	3
β-strand	142	1	4
β-strand	143	1	5
β-strand	150	1	4
β-strand	153	1	3
α-helix	164-166	3
β-strand	173	1	6
α-helix	174-176	3
β-strand	177-180	4	7
β-strand	187-190	4	7
β-strand	192	1	3
β-strand	193	1	6
α-helix	202-205	4

Chain B: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-14	5	9
β-strand	19-21	3	10
β-strand	22-25	4	8
β-strand	31-45	8	9
β-strand	49-58	10	9
β-strand	61-68	4	9
β-strand	76-78	3	10
β-strand	86	1	8
β-strand	89-91	3	10
α-helix	96-98	3
β-strand	101-107	7	9
α-helix	113-114	2
β-strand	115-116	2	9
β-strand	120-125	6	9
α-helix	128-130	3
β-strand	132	1	11
β-strand	135-139	5	5
α-helix	140-142	3
α-helix	143-148	6
β-strand	151-161	11	5
β-strand	162	1	11
β-strand	166-172	7	12
β-strand	175-177	3	12
β-strand	181-183	3	5
α-helix	187	1
β-strand	188-189	2	5
α-helix	197-198	2
β-strand	199-208	10	5
α-helix	209-213	5
β-strand	218-225	8	12
α-helix	239-240	2
β-strand	245-251	7	12

Chain C: 11 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	13
β-strand	25-32	8	13
β-strand	35-40	6	13
β-strand	48-49	2	13
α-helix	60-88	29
α-helix	91	1
α-helix	93	1
β-strand	94-104	11	13
α-helix	105	1
β-strand	110-118	9	13
β-strand	121-127	7	13
β-strand	130-133	4	13
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	14
α-helix	186-187	2
β-strand	188-193	6	15
β-strand	198	1	15
β-strand	201-209	9	15
β-strand	212	1	14
β-strand	216-221	6	16
β-strand	226	1	16
α-helix	227	1
β-strand	231	1	15
β-strand	236-237	2	15
β-strand	243-252	10	15
β-strand	260-265	6	16
β-strand	273-276	4	16

Chain D: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	17
β-strand	6-11	6	18
β-strand	21-30	10	18
β-strand	31	1	17
β-strand	36-41	6	19
β-strand	44-45	2	19
α-helix	46	1
β-strand	50-51	2	18
β-strand	55-56	2	18
β-strand	62-70	9	18
β-strand	78-83	6	19
β-strand	91-94	4	19
α-helix	95-96	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR Alpha Chain-TRAV12-3	A	protein	209	Homo sapiens	A0A0B4J271 (AlphaFold model), P01848 (AlphaFold model)
TCR Beta Chain-TRBV6-5	B	protein	243	Homo sapiens	A0A0K0K1A5 (AlphaFold model), A0A5B9 (AlphaFold model)
Antigen-presenting glycoprotein CD1d	C	protein	278	Homo sapiens	P15813
Beta-2-microglobulin	D	protein	119	Homo sapiens	P61769

Sequence of entity 1 (A), FASTA

>4WWK_1 TCR Alpha Chain-TRAV12-3 (chains A)
MQKEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDG
RFTAQVDKSSKYISLFIRDSQPSDSATYLCAMSGDLNTNAGKSTFGDGTTLTVKPNIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>4WWK_2 TCR Beta Chain-TRBV6-5 (chains B)
MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGE
VPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSQGPFQPQHFGDGTRLSILEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (C), FASTA

>4WWK_3 Antigen-presenting glycoprotein CD1d (chains C)
SPGVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYW

Sequence of entity 4 (D), FASTA

>4WWK_4 Beta-2-microglobulin (chains D)
MSRSVALAVLALLSLSGLEAIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLL
KNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

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
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Primary citation

Atypical natural killer T-cell receptor recognition of CD1d-lipid antigens. Le Nours, J., Praveena, T., Pellicci, D.G. et al. Nat Commun (2016) 7:10570-10570. DOI 10.1038/ncomms10570 · PubMed

Other PDB entries of the same protein (UniProt A0A0B4J271 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5C0C 1.97 Å, 1E6 TCR in complex with HLA-A02 carrying RQFGPDWIVA
5C0B 2.03 Å, 1E6 TCR in complex with HLA-A02 carrying RQFGPDFPTI
5C07 2.11 Å, 1E6 TCR in complex with HLA-A02 carrying YQFGPDFPIA
5C08 2.33 Å, 1E6 TCR in Complex with HLA-A0e carrying RQWGPDPAAV
5C0A 2.46 Å, 1E6 TCR in complex with HLA-A02 carrying MVW peptide
5C09 2.48 Å, HLA class I histocompatibility antigen
7FJE 3.0 Å, Cryo-EM structure of a membrane protein(LL)
5HYJ 3.06 Å, 1E6 TCR in Complex with HLA-A02 carrying AQWGPDPAAA
7FJF 3.1 Å, Cryo-EM structure of a membrane protein(CS)
7FJD 3.2 Å, Cryo-EM structure of a membrane protein(WT)
6JXR 3.7 Å, Structure of human T cell receptor-CD3 complex

Browse structure collections

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