2PYF: High Affinity Human T-Cell Receptors

Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC RevealNative Diagonal Binding Geometry Unbound TCR Clone 5-1. Determined by X-ray diffraction at 2.2 Å resolution. Released 25 Sept 2007.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,731
Mol. weight: 50.83 kDa
Released: 25 Sept 2007

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

Secondary structure: helices and β-sheets

2PYF contains 13 α-helices and 45 β-strands across 2 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: 5 helices, 17 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	30-38	9	2
β-strand	44-51	8	2
β-strand	56-59	4	1
β-strand	62-67	6	1
β-strand	72-77	6	1
α-helix	82-84	3
β-strand	86-94	9	2
β-strand	103-104	2	2
β-strand	108-113	6	2
α-helix	114-115	2
β-strand	122-128	7	3
β-strand	135-140	6	3
β-strand	156-158	3	3
α-helix	159-161	3
β-strand	162-166	5	3
α-helix	167-169	3
β-strand	171-180	10	3
α-helix	187-191	5
β-strand	200	1	3

Chain B: 8 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	4
β-strand	8-12	5	5
β-strand	17-19	3	6
β-strand	20-23	4	4
β-strand	29-36	8	5
β-strand	40-49	10	5
β-strand	52-55	4	5
β-strand	63-64	2	6
β-strand	71	1	4
β-strand	74-76	3	6
α-helix	81-83	3
β-strand	85-92	8	5
β-strand	96	1	7
β-strand	98	1	7
α-helix	99-100	2
β-strand	101-102	2	5
β-strand	106-111	6	5
α-helix	114-116	3
β-strand	118	1	8
β-strand	121-126	6	3
α-helix	127-128	2
α-helix	129-135	7
β-strand	137-147	11	3
β-strand	148	1	8
β-strand	152-158	7	9
β-strand	161-163	3	9
β-strand	167-169	3	3
α-helix	173	1
β-strand	174-175	2	3
β-strand	185-194	10	3
α-helix	195-199	5
β-strand	204-211	8	9
β-strand	214	1	10
α-helix	225-226	2
β-strand	228	1	10
β-strand	230-237	8	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T-Cell Receptor, Alpha Chain	A	protein	205	Homo sapiens	P01848 (AlphaFold model)
T-Cell Receptor, Beta Chain	B	protein	241	Homo sapiens	P01850 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2PYF_1 T-Cell Receptor, Alpha Chain (chains A)
KQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTSG
RLNASLDKSSGSSTLYIAASQPGDSATYLCAVRPLLDGTYIPTFGRGTSLIVHPYIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPDTFFPSPE

Sequence of entity 2 (B), FASTA

>2PYF_2 T-Cell Receptor, Beta Chain (chains B)
GVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGTTDQGEVPN
GYNVSRSTIEDFPLRLLSAAPSQTSVYFCASSYLGNTGELFFGEGSRLTVLEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

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 P01848 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UDT 1.35 Å, T cell receptor (TRAV22,TRBV7-9) structure
4WW1 1.38 Å, Crystal structure of human TCR Alpha Chain-TRAV21-TRAJ8 and Beta Chain-TRBV7-8
1OGA 1.4 Å, A structural basis for immunodominant human T-cell receptor recognition.
2BNU 1.4 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
1KGC 1.5 Å, Immune Receptor
2BNQ 1.7 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2BNR 1.9 Å, Structural and kinetic basis for heightened immunogenicity of T cell vaccines
2IAL 1.92 Å, Structural basis for recognition of mutant self by a tumor-specific, MHC class…
5C0C 1.97 Å, 1E6 TCR in complex with HLA-A02 carrying RQFGPDWIVA
2VLM 1.98 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5KSA 2.0 Å, Bel602-DQ8.5-glia-gamma1 complex
7RYL 2.0 Å, T cell receptor CO3

Browse structure collections

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