5ISZ: LS01-TCR/M1-HLA-A*02 complex

Crystal structure of LS01-TCR/M1-HLA-A*02 complex. Determined by X-ray diffraction at 2.06 Å resolution. Released 1 Mar 2017.

Method: X-ray diffraction
Resolution: 2.06 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 5
Atoms: 7,244
Mol. weight: 94.31 kDa
Released: 1 Mar 2017

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

Secondary structure: helices and β-sheets

5ISZ contains 23 α-helices and 73 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: 10 helices, 19 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	50-54	5
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	138-150	13
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	186-195	10	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	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 D: 5 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	32-38	7	9
β-strand	45-50	6	9
β-strand	56-59	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-93	8	9
β-strand	100-101	2	9
β-strand	105-110	6	9
α-helix	111-112	2
β-strand	119-125	7	10
β-strand	132-137	6	10
β-strand	153-154	2	10
α-helix	155-157	3
β-strand	158-162	5	10
α-helix	163-165	3
β-strand	167-175	9	10
α-helix	183-186	4
β-strand	197	1	10

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	11
β-strand	12-16	5	12
β-strand	21-23	3	13
β-strand	24-27	4	11
β-strand	33-39	7	12
β-strand	45-53	9	12
β-strand	56-59	4	12
β-strand	66-68	3	13
β-strand	75	1	11
β-strand	78-80	3	13
β-strand	89-96	8	12
β-strand	104-105	2	12
β-strand	109-114	6	12
α-helix	117-119	3
β-strand	121	1	14
α-helix	122-123	2
β-strand	124-129	6	10
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-150	11	10
β-strand	151	1	14
β-strand	155-161	7	15
β-strand	164-166	3	15
β-strand	170-172	3	10
β-strand	177-178	2	10
β-strand	188-197	10	10
α-helix	198-201	4
β-strand	207-214	8	15
β-strand	217	1	16
α-helix	228-229	2
β-strand	231	1	16
β-strand	233-240	8	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A	protein	275	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B	protein	98	Homo sapiens	P61769 (AlphaFold model)
influenza M1 for peptide	C	protein	9	Influenza A virus	P03485 (AlphaFold model)
TCRalpha chain	D	protein	200	Homo sapiens
TCRbeta chain	E	protein	241	Homo sapiens

Sequence of entity 1 (A), FASTA

>5ISZ_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>5ISZ_2 Beta-2-microglobulin (chains B)
QRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDWS
FYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>5ISZ_3 influenza M1 for peptide (chains C)
GILGFVFTL

Sequence of entity 4 (D), FASTA

>5ISZ_4 TCRalpha chain (chains D)
LNVEQSPQSLHVQEGDSTNFTCSFPSSNFYALHWYRWETAKSPEALFVMTLNGDEKKKGR
ISATLNTKEGYSYLYIKGSQPEDSATYLCAFDTNAGKSTFGDGTTLTVKPNIQNPDPAVY
QLRDSASSAKSVCLFTDFDSQTNVSQSKDDVYITDKCVLDMRSMDFKSNSAVAWSNKSDF
ACANAFNNSIIPEDTFFPSP

Sequence of entity 5 (E), FASTA

>5ISZ_5 TCRbeta chain (chains E)
IGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGDI
AAGYSVSREKKESFPLTVTSAQKNPTAFYLCASSIFGQREQYFGPGTRLTVTEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
A

Primary citation

Broad TCR repertoire and diverse structural solutions for recognition of an immunodominant CD8(+) T cell epitope. Song, I., Gil, A., Mishra, R. et al. Nat Struct Mol Biol (2017) 24:395-406. DOI 10.1038/nsmb.3383 · 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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