4WW2: TCR Alpha Chain-TRAV21-TRAJ8

Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8, Beta Chain-TRBV7-8, Antigen-presenting glycoprotein CD1d, and Beta-2-microglobulin. Determined by X-ray diffraction at 2.48 Å resolution. Released 3 Feb 2016.

Method: X-ray diffraction
Resolution: 2.48 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,540
Mol. weight: 95.29 kDa
Ligands: NAG, JLS
Released: 3 Feb 2016

Explore 4WW2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WW2 contains 22 α-helices and 72 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: 3 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	2
β-strand	19-25	7	1
β-strand	30-44	9	2
β-strand	50-57	8	2
β-strand	62-68	4	1
β-strand	76-81	6	1
β-strand	86-91	6	1
α-helix	96-98	3
β-strand	100-108	9	2
β-strand	115-116	2	2
β-strand	120-125	6	2
β-strand	134-139	6	3
β-strand	140	1	4
β-strand	147-152	6	3
α-helix	160-163	4
β-strand	168-170	3	3
α-helix	171-173	3
β-strand	174-177	4	3
β-strand	184-192	9	3
β-strand	213	1	3

Chain B: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	5
β-strand	10-14	5	6
β-strand	19-24	6	5
β-strand	31-44	7	6
β-strand	51-57	7	6
β-strand	60-67	4	6
β-strand	76-79	4	5
β-strand	87-91	5	5
α-helix	96-98	3
β-strand	100-107	8	6
β-strand	114-115	2	6
β-strand	119-124	6	6
α-helix	127-129	3
β-strand	131	1	7
β-strand	134-138	5	4
α-helix	139-141	3
α-helix	142-148	7
β-strand	150-160	11	4
β-strand	161	1	7
β-strand	165-171	7	8
β-strand	174-176	3	8
β-strand	180-182	3	4
α-helix	186	1
β-strand	187-188	2	4
β-strand	198-207	10	4
α-helix	208-212	5
β-strand	217-224	8	8
β-strand	227	1	9
α-helix	238-239	2
β-strand	241	1	9
β-strand	243-250	8	8

Chain C: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	10-18	9	10
β-strand	24-32	9	10
β-strand	35-40	6	10
α-helix	47	1
β-strand	48-49	2	10
α-helix	60-87	28
α-helix	91	1
β-strand	94-103	10	10
α-helix	109-110	2
β-strand	111-118	8	10
β-strand	121-127	7	10
β-strand	130-133	4	10
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	11
β-strand	188-194	7	12
β-strand	201-211	11	12
β-strand	212	1	11
β-strand	217-222	6	13
β-strand	225-226	2	13
β-strand	230-231	2	12
β-strand	236-237	2	12
β-strand	243-252	10	12
β-strand	260-264	5	13
α-helix	266-268	3
β-strand	273-276	4	13

Chain F: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	14
α-helix	4-5	2
β-strand	6-11	6	15
β-strand	21-30	10	15
β-strand	31	1	14
β-strand	36-41	6	16
β-strand	44-45	2	16
β-strand	50-51	2	15
α-helix	52-54	3
β-strand	55-56	2	15
β-strand	62-70	9	15
β-strand	78-83	6	16
β-strand	91-94	4	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
TCR Alpha Chain-TRAV21-TRAJ8	A	protein	207	Homo sapiens	A0A0B4J279 (AlphaFold model), P01848 (AlphaFold model)
TCR Beta Chain-TRBV7-8	B	protein	243	Homo sapiens	A0A5B9 (AlphaFold model)
Antigen-presenting glycoprotein CD1d	C	protein	284	Homo sapiens	P15813 (AlphaFold model)
Beta-2-microglobulin	F	protein	99	Homo sapiens	P61769

Sequence of entity 1 (A), FASTA

>4WW2_1 TCR Alpha Chain-TRAV21-TRAJ8 (chains A)
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGRSTLYIAASQPGDSATYLCAGVNTGFQKLVFGTGTRLLVSPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 2 (B), FASTA

>4WW2_2 TCR Beta Chain-TRBV7-8 (chains B)
MGAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQALGQGPEFLTYFQNEAQLDKSG
LPSDRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSSRDLEQYFGPGTRLTVTEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Sequence of entity 3 (C), FASTA

>4WW2_3 Antigen-presenting glycoprotein CD1d (chains C)
SPGVPQRLFPLRCLQISSFANSSWTRTDGLAWLGELQTHSWSNDSDTVRSLKPWSQGTFS
DQQWETLQHIFRVYRSSFTRDVKEFAKMLRLSYPLELQVSAGCEVHPGNASNNFFHVAFQ
GKDILSFQGTSWEPTQEAPLWVNLAIQVLNQDKWTRETVQWLLNGTCPQFVSGLLESGKS
ELKKQVKPKAWLSRGPSPGPGRLLLVCHVSGFYPKPVWVKWMRGEQEQQGTQPGDILPNA
DETWYLRATLDVVAGEAAGLSCRVKHSSLEGQDIVLYWHHHHHH

Sequence of entity 4 (F), FASTA

>4WW2_4 Beta-2-microglobulin (chains F)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Ligands and cofactors

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

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 A0A0B4J279 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WW1 1.38 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8
2BNU 1.4 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2BNQ 1.7 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
2BNR 1.9 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
5EU6 2.02 Å, HLA Class I antigen
2F53 2.1 Å, Directed Evolution of Human T-cell Receptor CDR2 residues by phage display dramatically…
2P5W 2.2 Å, Crystal structures of high affinity human T-cell receptors bound to pMHC reveal native…
2PYE 2.3 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative…
5BS0 2.4 Å, MAGE-A3 Reactive TCR in complex with Titin Epitope in HLA-A1
6Q3S 2.5 Å, Engineered Human HLA_A2 MHC Class I molecule in complex with TCR and SV9 peptide
5BRZ 2.62 Å, MAGE-A3 reactive TCR in complex with MAGE-A3 in HLA-A1

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