5YXN: A T cell receptor

A T cell receptor in complex with HLA-A0201 restricted Hepatitis C virus NS3 peptide (KLVALGINAV). Determined by X-ray diffraction at 2.03 Å resolution. Released 12 Dec 2018.

Method: X-ray diffraction
Resolution: 2.03 Å
Organisms: Homo sapiens, Hepatitis C virus
Chains: 5
Atoms: 7,158
Mol. weight: 93.87 kDa
Released: 12 Dec 2018

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

Secondary structure: helices and β-sheets

5YXN contains 23 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: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	11-15	5	2
β-strand	20-22	3	1
β-strand	25-27	3	1
β-strand	34-40	7	2
β-strand	47-53	7	2
α-helix	59-60	2
β-strand	61-62	2	1
β-strand	65-70	6	1
β-strand	75-80	6	1
α-helix	85-87	3
β-strand	89-96	8	2
β-strand	101-103	3	2
β-strand	107-112	6	2
β-strand	121-125	5	3
β-strand	126-127	2	4
β-strand	135-139	5	3
β-strand	156-157	2	3
α-helix	158-160	3
β-strand	161-165	5	3
α-helix	166-168	3
β-strand	170-178	9	3

Chain B: 5 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	5
β-strand	11-15	5	6
β-strand	20-22	3	7
β-strand	23-26	4	5
β-strand	32-38	7	6
β-strand	44-50	7	6
β-strand	57-58	2	6
β-strand	65-67	3	7
β-strand	71	1	5
β-strand	74	1	5
β-strand	77-79	3	7
α-helix	84-86	3
β-strand	88-95	8	6
β-strand	101-103	3	6
β-strand	107-112	6	6
β-strand	119	1	8
α-helix	120-121	2
β-strand	122-127	6	4
α-helix	128-129	2
α-helix	130-136	7
β-strand	138-148	11	4
β-strand	149	1	8
β-strand	153-159	7	9
β-strand	162-164	3	9
β-strand	168-170	3	4
β-strand	175-176	2	4
β-strand	186-195	10	4
α-helix	196-199	4
β-strand	205-212	8	9
β-strand	215	1	10
β-strand	229	1	10
β-strand	231-238	8	9

Chain C: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	11
α-helix	21	1
β-strand	22-29	8	11
β-strand	32-38	7	11
β-strand	47-48	2	11
α-helix	52-55	4
α-helix	58-85	28
β-strand	95-104	10	11
β-strand	110-119	10	11
β-strand	122-127	6	11
β-strand	134-136	3	11
α-helix	139-150	12
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-175	11
α-helix	177-180	4
β-strand	184	1	12
α-helix	185-186	2
β-strand	187-194	8	13
β-strand	199-209	11	13
β-strand	210	1	12
β-strand	215-220	6	14
β-strand	223-224	2	14
β-strand	229-231	3	13
α-helix	232-234	3
β-strand	235-236	2	13
β-strand	242-251	10	13
α-helix	255-257	3
β-strand	258-263	6	14
β-strand	271-273	3	14

Chain D: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	15
α-helix	6-7	2
β-strand	8-13	6	16
β-strand	23-32	10	16
β-strand	33	1	15
β-strand	38-43	6	17
β-strand	46-47	2	17
α-helix	48	1
β-strand	52-53	2	16
α-helix	54-56	3
β-strand	57-58	2	16
β-strand	64-72	9	16
β-strand	80-85	6	17
β-strand	93-96	4	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
T cell receptor alpha chain	A	protein	192	Homo sapiens
T cell receptor beta chain	B	protein	241	Homo sapiens
HLA class I histocompatibility antigen, A-2 alpha chain	C	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	D	protein	100	Homo sapiens	P61769 (AlphaFold model)
NS3 peptide	I	protein	10	Hepatitis C virus	P27958 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5YXN_1 T cell receptor alpha chain (chains A)
AQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQPPSRQMILVIRQEAYKQQNAT
ENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAYGEDDKIIFGKGTRLHILPNIQNPDPA
VYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNK
SDFACANAFNNS

Sequence of entity 2 (B), FASTA

>5YXN_2 T cell receptor beta chain (chains B)
AADIYQTPRYLVIGTGKKITLECSQTMGHDKMYWYQQDPGMELHLIHYSYGVNSTEKGDL
SSESTVSRIRTEHFPLTLESARPSHTSQYLCASRRGPYEQYFGPGTRLTVTEDLKNVFPP
EVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPAL
NDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA
D

Sequence of entity 3 (C), FASTA

>5YXN_3 HLA class I histocompatibility antigen, A-2 alpha chain (chains C)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 4 (D), FASTA

>5YXN_4 Beta-2-microglobulin (chains D)
GIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSEIEVDLLKNGERIEKVEHSDLSFSED
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 5 (I), FASTA

>5YXN_5 NS3 peptide (chains I)
KLVALGINAV

Primary citation

Capturing HCV immune escape by targeting structural based mechanism. Hui, F. To be published.

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

Browse structure collections

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