6RPB: T-cell receptor NYE_S1

Crystal structure of the T-cell receptor NYE_S1 bound to HLA A2*01-SLLMWITQV. Determined by X-ray diffraction at 2.5 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 20
Atoms: 26,194
Mol. weight: 381.19 kDa
Released: 15 Jan 2020

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

Secondary structure: helices and β-sheets

6RPB contains 113 α-helices and 298 β-strands across 20 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: 9 helices, 18 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	57-85	29
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	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-273	4	4

Chains B, G, L and Q: 4 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	36-41	6	7
β-strand	44-45	2	7
α-helix	46	1
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
α-helix	90	1
β-strand	91-94	4	7

Chains C, H, M and R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6	1	8

Chain D: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	11-14	4	10
α-helix	18	1
β-strand	19-25	7	9
β-strand	36-44	9	10
β-strand	51-56	6	10
β-strand	64-68	5	9
β-strand	76-81	6	9
β-strand	86-91	6	9
α-helix	96-98	3
β-strand	100-108	9	10
α-helix	116	1
β-strand	117-118	2	10
α-helix	119	1
β-strand	122-127	6	10
β-strand	136-139	4	11
β-strand	149-154	6	11
α-helix	160-162	3
β-strand	171-172	2	11
α-helix	173-175	3
β-strand	176-180	5	11
α-helix	181-183	3
β-strand	185-194	10	11
β-strand	215	1	11

Chains E, J and T: 9 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	38-45	8	13
β-strand	49-58	10	13
β-strand	65-68	4	13
β-strand	76-78	3	14
β-strand	86	1	12
β-strand	89-91	3	14
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	109	1	8
α-helix	114-116	3
β-strand	117-118	2	13
β-strand	122-127	6	13
α-helix	131-133	3
β-strand	135	1	15
α-helix	136-137	2
β-strand	138-142	5	16
α-helix	143-145	3
α-helix	146-152	7
β-strand	154-164	11	16
β-strand	165	1	15
β-strand	169-175	7	17
β-strand	178-180	3	17
β-strand	184-186	3	16
α-helix	190	1
β-strand	191-192	2	16
β-strand	202-211	10	16
α-helix	212-216	5
β-strand	221-228	8	17
β-strand	231	1	18
α-helix	242-243	2
β-strand	245	1	18
β-strand	247-254	8	17

Chain F: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	19
β-strand	21-28	8	19
β-strand	31-37	7	19
β-strand	46-47	2	19
α-helix	57-85	29
β-strand	94-103	10	19
β-strand	109-118	10	19
β-strand	121-126	6	19
β-strand	133-135	3	19
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	20
α-helix	184-185	2
β-strand	186-193	8	21
β-strand	198-208	11	21
β-strand	209	1	20
β-strand	214-219	6	22
β-strand	222-223	2	22
β-strand	228-230	3	21
α-helix	231-233	3
β-strand	234-235	2	21
β-strand	241-250	10	21
α-helix	254-256	3
β-strand	257-262	6	22
β-strand	270-273	4	22

Chain I: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	27
β-strand	11-14	4	28
α-helix	18	1
β-strand	19-25	7	27
β-strand	36-44	9	28
β-strand	51-56	6	28
β-strand	64-68	5	27
β-strand	76-81	6	27
β-strand	86-91	6	27
α-helix	96-98	3
β-strand	100-108	9	28
α-helix	116	1
β-strand	117-118	2	28
α-helix	119	1
β-strand	122-127	6	28
β-strand	136-140	5	29
β-strand	149-154	6	29
α-helix	160-162	3
β-strand	171-172	2	29
α-helix	173-175	3
β-strand	176-180	5	29
α-helix	181-183	3
β-strand	185-194	10	29
β-strand	215	1	29

Chain K: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	37
β-strand	21-28	8	37
β-strand	31-37	7	37
β-strand	46-47	2	37
α-helix	57-85	29
β-strand	94-103	10	37
β-strand	109-118	10	37
β-strand	121-126	6	37
β-strand	133-135	3	37
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	38
α-helix	184-185	2
β-strand	186-192	7	39
β-strand	200-208	9	39
β-strand	209	1	38
β-strand	214-219	6	40
β-strand	229-230	2	39
α-helix	231-233	3
β-strand	234-235	2	39
β-strand	241-248	8	39
β-strand	257-262	6	40
β-strand	270-273	4	40

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, F, K, P	protein	277	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G, L, Q	protein	100	Homo sapiens	P61769 (AlphaFold model)
Heteroclitic NY-ESO-1 157-165 peptide	C, H, M, R	protein	9	Homo sapiens	P78358 (AlphaFold model)
T-cell receptor alpha chain	D, I, N, S	protein	206	Homo sapiens
T-cell receptor beta chain	E, J, O, T	protein	244	Homo sapiens

Sequence of entity 1 (A, F, K, P), FASTA

>6RPB_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, F, K, P)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G, L, Q), FASTA

>6RPB_2 Beta-2-microglobulin (chains B, G, L, Q)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H, M, R), FASTA

>6RPB_3 Heteroclitic NY-ESO-1 157-165 peptide (chains C, H, M, R)
SLLMWITQV

Sequence of entity 4 (D, I, N, S), FASTA

>6RPB_4 T-cell receptor alpha chain (chains D, I, N, S)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSDGDKEDG
RFTAQLNRASQYVSLLIRDSQPSDSATYLCAVKSGGSYIPTFGRGTSLIVHPYIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E, J, O, T), FASTA

>6RPB_5 T-cell receptor beta chain (chains E, J, O, T)
MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDKGE
VPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYLNRDSALDFGPGTRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

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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