6RPA: T-cell receptor NYE_S2

Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV. Determined by X-ray diffraction at 2.56 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.56 Å
Organism: Homo sapiens
Chains: 5
Atoms: 6,326
Mol. weight: 95.87 kDa
Released: 15 Jan 2020

Explore 6RPA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RPA contains 24 α-helices and 73 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	3-12	10	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-53	4
α-helix	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	230	1	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	272	1	4

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
α-helix	14-15	2
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain D: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	8
β-strand	10-14	5	9
β-strand	19-21	3	10
β-strand	24-27	4	8
β-strand	37-44	8	9
α-helix	50	1
β-strand	51-56	6	9
β-strand	64-66	3	10
β-strand	77-79	3	10
β-strand	81	1	8
β-strand	86	1	8
β-strand	89-91	3	10
α-helix	96-98	3
β-strand	100-108	9	9
β-strand	117-118	2	9
β-strand	122-127	6	9
α-helix	128-129	2
β-strand	136-142	7	11
β-strand	149-154	6	11
β-strand	176-177	2	12
β-strand	188-189	2	12
β-strand	191	1	11

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-25	7	13
β-strand	38-44	7	14
β-strand	50-55	6	14
α-helix	64-65	2
β-strand	66-67	2	14
α-helix	68	1
β-strand	78-79	2	13
β-strand	86-91	6	13
α-helix	96-98	3
β-strand	100-107	8	14
β-strand	117	1	14
β-strand	123-127	5	14
α-helix	130-132	3
β-strand	134	1	15
α-helix	135-136	2
β-strand	137-142	6	11
α-helix	143-144	2
α-helix	145-151	7
β-strand	153-163	11	11
β-strand	164	1	15
β-strand	168-174	7	16
β-strand	177-179	3	16
β-strand	183-185	3	11
β-strand	190-191	2	11
β-strand	201-210	10	11
α-helix	211-215	5
β-strand	221-227	7	16
β-strand	230	1	17
β-strand	244	1	17
β-strand	246-251	6	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	277	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Heteroclitic NY-ESO-1 157-165 peptide	C	protein	9	Homo sapiens	P78358 (AlphaFold model)
T-cell receptor alpha chain	D	protein	212	Homo sapiens
T-cell receptor beta chain	E	protein	246	Homo sapiens

Sequence of entity 1 (A), FASTA

>6RPA_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>6RPA_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6RPA_3 Heteroclitic NY-ESO-1 157-165 peptide (chains C)
SLLMWITQV

Sequence of entity 4 (D), FASTA

>6RPA_4 T-cell receptor alpha chain (chains D)
MAQSVAQPEDQVNVAEGNPLTVKCTYSVSGNPYLFWYVQYPNRGLQFLLKYITGDNLVKG
SYGFEAEFNKSQTSFHLKKPSALVSDSALYFCAVRDINSGAGSYQLTFGKGTKLSVIPNI
QNPDPAVYQLRDSDSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSA
VAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>6RPA_5 T-cell receptor beta chain (chains E)
MSAVISQKPSRDIKQRGTSLTIQCQVDSQVTMMFWYRQQPGQSLTLIATANQGSEATYES
GFVIDKFPISRPNLTFSTLTVSNMSPEDSSIYLCSVGGSGGADTQYFGPGTRLTVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Primary citation

TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex. Coles, C.H., Mulvaney, R.M., Malla, S. et al. J Immunol (2020) 204:1943-1953. DOI 10.4049/jimmunol.1900915 · PubMed

Other PDB entries of the same protein (UniProt P04439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
3D25 1.3 Å, Crystal structure of HA-1 minor histocompatibility antigen bound to human class I MHC…
3MRG 1.3 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCV NS3-1073-1081…
6JOZ 1.35 Å, Crystal structure of BRLF peptide from EBV in complex with HLA-A1101.
5C0G 1.37 Å, HLA-A02 carrying YLGGPDFPTI
5N1Y 1.39 Å, HLA-A02 carrying MVWGPDPLYV
1I4F 1.4 Å, Crystal structure of HLA-A*0201/MAGE-A4-peptide complex
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
3MRB 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with HCMV pp65-495-503…
3MRK 1.4 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with AFP137 nonapeptide
6J2A 1.4 Å, The structure of HLA-A*3003/NP44
1X7Q 1.45 Å, Crystal structure of HLA-A*1101 with sars nucleocapsid peptide

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