2PYE: High Affinity Human T-Cell Receptors

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry TCR Clone C5C1 Complexed with MHC. Determined by X-ray diffraction at 2.3 Å resolution. Released 25 Sept 2007.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,134
Mol. weight: 96.01 kDa
Ligands: 7PE
Released: 25 Sept 2007

Explore 2PYE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2PYE contains 28 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: 11 helices, 20 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	57-84	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	1	3
β-strand	189-192	4	4
β-strand	198-208	11	4
β-strand	209	1	2
β-strand	214-219	6	5
β-strand	222-223	2	5
β-strand	228-230	3	4
α-helix	231-233	3
β-strand	234-235	2	4
β-strand	241-250	10	4
α-helix	254-256	3
β-strand	257-262	6	5
β-strand	270-273	4	5

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
α-helix	4-5	2
β-strand	6-11	6	7
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-83	6	8
α-helix	90	1
β-strand	91-94	4	8

Chain D: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	10-14	5	10
α-helix	17-18	2
β-strand	19-25	7	9
β-strand	30-38	9	10
β-strand	44-51	8	10
β-strand	56-59	4	9
β-strand	62-67	6	9
α-helix	68-70	3
β-strand	72-77	6	9
α-helix	82-84	3
β-strand	86-94	9	10
β-strand	103-104	2	10
β-strand	108-113	6	10
α-helix	114	1
β-strand	122-127	6	11
β-strand	128	1	12
β-strand	132	1	13
β-strand	134	1	13
β-strand	135-140	6	11
α-helix	149-151	3
β-strand	156-158	3	11
α-helix	159-161	3
β-strand	162-166	5	11
α-helix	167-169	3
β-strand	171-180	10	11
α-helix	187-189	3

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	14
β-strand	8-12	5	15
β-strand	17-19	3	16
β-strand	20-23	4	14
β-strand	29-35	7	15
β-strand	41-47	7	15
β-strand	54-55	2	15
β-strand	62-64	3	16
β-strand	71	1	14
β-strand	74-76	3	16
α-helix	81-83	3
β-strand	85-92	8	15
β-strand	101-102	2	15
β-strand	106-111	6	15
α-helix	114-116	3
β-strand	118	1	17
β-strand	121-125	5	12
α-helix	126-128	3
α-helix	129-135	7
β-strand	137-147	11	12
β-strand	148	1	17
β-strand	152-158	7	18
β-strand	161-163	3	18
β-strand	167-169	3	12
β-strand	174-175	2	12
β-strand	185-194	10	12
α-helix	195-198	4
β-strand	204-211	8	18
β-strand	214	1	19
α-helix	225-226	2
β-strand	228	1	19
β-strand	230-237	8	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	276	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Cancer/testis antigen 1B	C	protein	9		P78358 (AlphaFold model)
T-Cell Receptor, Alpha Chain	D	protein	195	Homo sapiens	A0A0B4J279 (AlphaFold model)
T-Cell Receptor, Beta Chain	E	protein	242	Homo sapiens	P01850

Sequence of entity 1 (A), FASTA

>2PYE_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B), FASTA

>2PYE_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPCIVKWDRDM

Sequence of entity 3 (C), FASTA

>2PYE_3 Cancer/testis antigen 1B (chains C)
SLLMWITQC

Sequence of entity 4 (D), FASTA

>2PYE_4 T-Cell Receptor, Alpha Chain (chains D)
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGSSTLYIAASQPGDSATYLCAVRPLLDGTYIPTFGRGTSLIVHPYIQNP
DPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAW
SNKSDFACANAFNNS

Sequence of entity 5 (E), FASTA

>2PYE_5 T-Cell Receptor, Beta Chain (chains E)
MGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGTTDQGEVP
NGYNVSRSTIEDFPLRLLSAAPSQTSVYFCASSYLGNTGELFFGEGSRLTVLEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
7PE	2-(2-(2-(2-(2-(2-ethoxyethoxy)ethoxy)ethoxy)ethoxy)ethoxy)ethanol	C14 H30 O7	1

Water and common crystallization additives (GOL, PGE, SO4) are not listed.

Primary citation

Crystal structures of high affinity human T-cell receptors bound to peptide major histocompatibility complex reveal native diagonal binding geometry. Sami, M., Rizkallah, P.J., Dunn, S. et al. Protein Eng Des Sel (2007) 20:397-403. DOI 10.1093/protein/gzm033 · PubMed

Other PDB entries of the same protein (UniProt A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
7QPJ 1.54 Å, Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10…
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
7MKB 1.9 Å, Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL

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