6RP9: T-cell receptor NYE_S3

Crystal structure of the T-cell receptor NYE_S3 bound to HLA A2*01-SLLMWITQV. Determined by X-ray diffraction at 3.12 Å resolution. Released 15 Jan 2020.

Method: X-ray diffraction
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 12
Atoms: 16,633
Mol. weight: 241.5 kDa
Released: 15 Jan 2020

Explore 6RP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RP9 contains 53 α-helices and 188 β-strands across 11 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
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	51-54	4
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
α-helix	183-185	3
β-strand	186	1	2
β-strand	189-192	4	3
β-strand	198-208	11	3
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
β-strand	257-262	6	4
β-strand	270-273	4	4

Chain B: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6	1	6
α-helix	7	1
β-strand	9-11	3	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
β-strand	91-94	4	7

Chain C: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3

Chain D: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	8
β-strand	11-14	4	9
α-helix	18	1
β-strand	19-24	6	8
β-strand	38-44	7	10
β-strand	51-56	6	10
β-strand	64-68	5	8
β-strand	76-81	6	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	101-107	7	10
β-strand	116-118	3	10
β-strand	122-123	2	10
β-strand	124-127	4	9
β-strand	136-141	6	11
β-strand	142	1	12
β-strand	149-156	8	11
β-strand	170-172	3	11
β-strand	176-180	5	11
β-strand	185-194	10	11
β-strand	215	1	11

Chain E: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	14
β-strand	19-24	6	13
β-strand	29-44	9	14
β-strand	51-57	7	14
β-strand	64-65	2	14
β-strand	76-79	4	13
β-strand	87-91	5	13
α-helix	96-98	3
β-strand	100-109	10	14
β-strand	117-118	2	14
β-strand	122-127	6	14
α-helix	130-132	3
β-strand	134	1	15
β-strand	137	1	12
β-strand	140-141	2	12
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	12
β-strand	164	1	15
β-strand	168-174	7	16
β-strand	178-179	2	16
β-strand	183-185	3	12
β-strand	190-191	2	12
β-strand	201-210	10	12
α-helix	211-215	5
β-strand	220-227	8	16
β-strand	230	1	17
α-helix	241-242	2
β-strand	244	1	17
β-strand	246-253	8	16

Chain F: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	52-54	3
α-helix	57-85	29
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
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
α-helix	183-185	3
β-strand	186	1	19
β-strand	189-192	4	19
β-strand	198-208	11	19
β-strand	214-219	6	20
β-strand	222-223	2	20
β-strand	228-230	3	19
β-strand	234-235	2	19
β-strand	241-250	10	19
β-strand	257-262	6	20
β-strand	270-272	3	20

Chain G: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	21
α-helix	4-5	2
β-strand	6	1	22
β-strand	9-11	3	22
β-strand	21-30	10	22
β-strand	31	1	21
β-strand	36-41	6	23
β-strand	44-45	2	23
β-strand	50-51	2	22
α-helix	52-54	3
β-strand	55-56	2	22
β-strand	62-70	9	22
β-strand	78-83	6	23
β-strand	91-94	4	23

Chain I: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	24
α-helix	7-8	2
β-strand	11-14	4	25
β-strand	19-24	6	24
β-strand	38-44	7	26
β-strand	51-56	6	26
β-strand	64-68	5	24
β-strand	76-81	6	24
β-strand	86-91	6	24
α-helix	96-98	3
β-strand	101-107	7	26
β-strand	116-118	3	26
β-strand	122-123	2	26
β-strand	124-127	4	25
α-helix	128	1
β-strand	136-141	6	27
β-strand	142	1	28
β-strand	149-156	8	27
β-strand	170-172	3	27
β-strand	176-180	5	27
β-strand	185-194	10	27
β-strand	215	1	27

3 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	protein	277	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Cancer/testis antigen 1	C, H	protein	9	Homo sapiens	P78358 (AlphaFold model)
T-cell receptor alpha chain	D, I, K	protein	206	Homo sapiens
T-cell receptor beta chain	E, J, L	protein	246	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>6RP9_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, F)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>6RP9_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>6RP9_3 Cancer/testis antigen 1 (chains C, H)
SLLMWITQV

Sequence of entity 4 (D, I, K), FASTA

>6RP9_4 T-cell receptor alpha chain (chains D, I, K)
MQKEVEQNSGPLSVPEGAIASLNCTYSDRGSQSFFWYRQYSGKSPELIMFIYSNGDKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCALTRGPGNQFYFGTGTSLTVIPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E, J, L), FASTA

>6RP9_5 T-cell receptor beta chain (chains E, J, L)
MGAGVSQSPRYKVTKRGQDVALRCDPISGHVSLYWYRQALGQGPEFLTYFNYEAQQDKSG
LPNDRFSAERPEGSISTLTIQRTEQRDSAMYRCASSSPGGVSTEAFFGQGTRLTVVEDLN
KVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
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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