5TEZ: TCR F50 recgonizing M1-HLA-A2

TCR F50 recgonizing M1-HLA-A2. Determined by X-ray diffraction at 1.7 Å resolution. Released 27 Sept 2017.

Method: X-ray diffraction
Resolution: 1.7 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 5
Atoms: 7,466
Mol. weight: 95.47 kDa
Released: 27 Sept 2017

Explore 5TEZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TEZ contains 27 α-helices and 75 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	1
α-helix	19-20	2
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
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	133-134	2	1
α-helix	138-140	3
α-helix	141-149	9
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	186-194	9	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-224	3	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	270-272	3	4

Chain B: 2 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
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 I: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	8
β-strand	11-15	5	9
β-strand	20-26	7	8
β-strand	33-39	7	9
β-strand	46-52	7	9
β-strand	57-60	4	8
β-strand	63-68	6	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	87-91	5	9
β-strand	92-97	6	10
β-strand	100-105	6	10
β-strand	109-114	6	9
β-strand	123-128	6	11
β-strand	129	1	12
β-strand	136-141	6	11
α-helix	150-152	3
β-strand	157-159	3	11
α-helix	160-162	3
β-strand	163-167	5	11
α-helix	168-170	3
β-strand	172-181	10	11
α-helix	188-190	3
β-strand	202	1	11

Chain J: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	22-25	4	13
β-strand	31-38	8	14
β-strand	42-51	10	14
β-strand	54-57	4	14
β-strand	65-66	2	15
β-strand	73	1	13
β-strand	76-78	3	15
α-helix	83-85	3
β-strand	87-94	8	14
α-helix	101-102	2
β-strand	103-104	2	14
β-strand	108-113	6	14
α-helix	116-118	3
β-strand	120	1	16
α-helix	121-122	2
β-strand	123-127	5	12
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	12
β-strand	150	1	16
β-strand	154-160	7	17
β-strand	163-165	3	17
β-strand	169-171	3	12
β-strand	176-177	2	12
β-strand	187-196	10	12
α-helix	197-200	4
β-strand	206-213	8	17
β-strand	216	1	18
α-helix	227-228	2
β-strand	230	1	18
β-strand	232-239	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gly-ile-leu-gly-phe-val-phe-thr-leu	C	protein	9	Influenza A virus	P03485 (AlphaFold model)
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
TCR F50 alpha chain	I	protein	208	Homo sapiens
TCR F50 beta chain	J	protein	243	Homo sapiens

Sequence of entity 1 (C), FASTA

>5TEZ_1 GLY-ILE-LEU-GLY-PHE-VAL-PHE-THR-LEU (chains C)
GILGFVFTL

Sequence of entity 2 (A), FASTA

>5TEZ_2 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 3 (B), FASTA

>5TEZ_3 Beta-2-microglobulin (chains B)
AIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (I), FASTA

>5TEZ_4 TCR F50 alpha chain (chains I)
GENVEQHPSTLSVQEGDSAVIKCTYSDSASNYFPWYKQELGKRPQLIIDIRSNVGEKKDQ
RIAVTLNKTAKHFSLHITETQPEDSAVYFCAASFIIQGAQKLVFGQGTRLTINPNIQNPD
PAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWS
NKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (J), FASTA

>5TEZ_5 TCR F50 beta chain (chains J)
EAQVTQNPRYLITVTGKKLTVTCSQNMNHEYMSWYRQDPGLGLRQIYYSMNVEVTDKGDV
PEGYKVSRKEKRNFPLILESPSPNQTSLYFCASSLLGGWSEAFFGQGTRLTVTEDLKNVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

Structural basis for clonal diversity of the human T-cell response to a dominant influenza virus epitope. Yang, X., Chen, G., Weng, N.P. et al. J Biol Chem (2017) 292:18618-18627. DOI 10.1074/jbc.M117.810382 · PubMed

Other PDB entries of the same protein (UniProt P03485 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2VLL 1.6 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5ISZ 2.06 Å, Crystal structure of LS01-TCR/M1-HLA-A*02 complex
1AA7 2.08 Å, Influenza virus matrix protein crystal structure at PH 4.0
5CQE 2.1 Å, 2.1 Angstrom resolution crystal structure of matrix protein 1 (M1; residues 1-164) from…
5EUO 2.1 Å, PF6-M1-HLA-A2
1EA3 2.3 Å, Influenza virus M1 protein
2VLR 2.3 Å, The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are…
5JHD 2.46 Å, Crystal structure of LS10-TCR/M1-HLA-A*02 complex
1HHI 2.5 Å, The antigenic identity of peptide(slash)mhc complexes: a comparison of the conformation…
3VDX 3.0 Å, Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains
7JM3 3.4 Å, Full-length three-dimensional structure of the influenza A virus M1 protein and its…
4IQ4 3.5 Å, Structure of a 16 nm protein cage designed by fusing symmetric oligomeric domains,…

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