5JHD: LS10-TCR/M1-HLA-A*02 complex

Crystal structure of LS10-TCR/M1-HLA-A*02 complex. Determined by X-ray diffraction at 2.46 Å resolution. Released 1 Mar 2017.

Method: X-ray diffraction
Resolution: 2.46 Å
Organisms: Homo sapiens, Influenza A virus
Chains: 10
Atoms: 13,492
Mol. weight: 192.64 kDa
Ligands: EDT
Released: 1 Mar 2017

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

Secondary structure: helices and β-sheets

5JHD contains 45 α-helices and 147 β-strands across 8 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	3-14	12	1
β-strand	18-28	11	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	133-135	3	1
α-helix	138-149	12
α-helix	152-157	6
α-helix	158-163	6
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	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
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	258-262	5	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: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	10-14	5	9
β-strand	19-21	3	8
β-strand	24-25	2	8
β-strand	32-39	8	9
β-strand	46-52	7	9
α-helix	56-57	2
β-strand	65-69	5	8
β-strand	74-79	6	8
α-helix	84-86	3
β-strand	88-96	9	9
β-strand	107-108	2	9
β-strand	112-117	6	9
β-strand	126-131	6	10
β-strand	139-144	6	10
β-strand	161-162	2	10
α-helix	163-165	3
β-strand	166-170	5	10
α-helix	171-173	3
β-strand	175-184	10	10
β-strand	205	1	10

Chain E: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	11
β-strand	12-15	4	12
β-strand	21-23	3	13
β-strand	24-27	4	11
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-59	2	12
β-strand	66-68	3	13
β-strand	75	1	11
β-strand	78-80	3	13
β-strand	89-97	9	12
β-strand	100-104	5	12
β-strand	108-112	5	12
α-helix	116-118	3
β-strand	120	1	14
α-helix	121-122	2
β-strand	123-127	5	15
α-helix	128-130	3
α-helix	131-137	7
β-strand	139-149	11	15
β-strand	150	1	14
β-strand	154-160	7	16
β-strand	163-165	3	16
β-strand	169-171	3	15
β-strand	176-177	2	15
β-strand	187-196	10	15
α-helix	197-201	5
β-strand	206-213	8	16
β-strand	216	1	17
α-helix	227-228	2
β-strand	230	1	17
β-strand	232-239	8	16

Chain F: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	46-47	2	18
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	18
β-strand	109-118	10	18
β-strand	121-126	6	18
β-strand	133-135	3	18
α-helix	138-149	12
α-helix	152-157	6
α-helix	158-163	6
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	19
α-helix	184-185	2
β-strand	186-193	8	20
β-strand	198-208	11	20
β-strand	209	1	19
β-strand	214-219	6	21
β-strand	222-223	2	21
β-strand	228-230	3	20
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-250	10	20
α-helix	254-256	3
β-strand	258-262	5	21
β-strand	270-272	3	21

Chain G: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	22
α-helix	4-5	2
β-strand	6-11	6	23
β-strand	21-30	10	23
β-strand	31	1	22
β-strand	36-41	6	24
β-strand	44-45	2	24
β-strand	50-51	2	23
α-helix	52-54	3
β-strand	55-56	2	23
β-strand	62-70	9	23
β-strand	78-83	6	24
α-helix	90	1
β-strand	91-94	4	24

Chain I: 3 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	25
β-strand	10-14	5	26
β-strand	19-21	3	25
β-strand	24-26	3	25
β-strand	32-39	8	26
β-strand	46-52	7	26
α-helix	56-57	2
β-strand	65-69	5	25
β-strand	74-79	6	25
α-helix	84-86	3
β-strand	88-96	9	26
β-strand	107-108	2	26
β-strand	112-117	6	26
β-strand	126-131	6	27
β-strand	139-144	6	27
β-strand	160-162	3	27
α-helix	163-165	3
β-strand	166-170	5	27
β-strand	175-184	10	27
β-strand	205	1	27

Chain J: 6 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	28
β-strand	12-16	5	29
β-strand	21-23	3	30
β-strand	24-27	4	28
β-strand	33-39	7	29
β-strand	45-51	7	29
β-strand	58-59	2	29
β-strand	66-68	3	30
β-strand	75	1	28
β-strand	78-80	3	30
β-strand	89-97	9	29
β-strand	100-104	5	29
β-strand	108-113	6	29
α-helix	116-118	3
β-strand	120	1	31
α-helix	121-122	2
β-strand	123-127	5	32
β-strand	128	1	27
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	32
β-strand	150	1	31
β-strand	154-160	7	33
β-strand	163-165	3	33
β-strand	169-171	3	32
β-strand	176-177	2	32
β-strand	187-196	10	32
α-helix	197-201	5
β-strand	206-213	8	33
β-strand	216	1	34
α-helix	227-228	2
β-strand	230	1	34
β-strand	232-239	8	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, F	protein	276	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Influenza M1(58-66) peptide	C, H	protein	9	Influenza A virus	P03485 (AlphaFold model)
TCRalpha chain	D, I	protein	213	Homo sapiens
TCRbeta chain	E, J	protein	242	Homo sapiens

Sequence of entity 1 (A, F), FASTA

>5JHD_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, F)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEA

Sequence of entity 2 (B, G), FASTA

>5JHD_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>5JHD_3 Influenza M1(58-66) peptide (chains C, H)
GILGFVFTL

Sequence of entity 4 (D, I), FASTA

>5JHD_4 TCRalpha chain (chains D, I)
MIQTVTQSQPEMSVQEAETVTLSCTYDTSESDYYLFWYKQPPSRQMILVIRQEAYKQQNA
TENRFSVNFQKAAKSFSLKISDSQLGDAAMYFCAWGVNAGGTSYGKLTFGQGTILTVHPN
IQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNS
AVAWSNKSDFACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E, J), FASTA

>5JHD_5 TCRbeta chain (chains E, J)
MIGGITQSPKYLFRKEGQNVTLSCEQNLNHDAMYWYRQDPGQGLRLIYYSQIVNDFQKGD
IAEGYSVSREKKESFPLTVTSAQKNPTAFYLCASSIGVYGYTFGSGTRLTVVEDLKNVFP
PEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPA
LNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGR
AD

Ligands and cofactors

ID	Name	Formula	Copies
EDT	{[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid	C10 H16 N2 O8	2

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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