5C07: 1E6 TCR

1E6 TCR in complex with HLA-A02 carrying YQFGPDFPIA. Determined by X-ray diffraction at 2.11 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 10
Atoms: 14,183
Mol. weight: 192.92 kDa
Released: 4 May 2016

Explore 5C07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5C07 contains 43 α-helices and 145 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: 9 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	138-150	13
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	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	257-262	6	4
β-strand	270-272	3	4

Chains B and G: 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: 2 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
β-strand	11-14	4	9
β-strand	19-25	7	8
β-strand	32-38	7	9
β-strand	45-51	7	9
β-strand	55-58	4	8
β-strand	61-66	6	8
β-strand	71-76	6	8
α-helix	81-83	3
β-strand	85-92	8	9
β-strand	100-101	2	9
β-strand	105-110	6	9
α-helix	111-112	2
β-strand	119	1	10
β-strand	123-124	2	11
β-strand	125	1	12
β-strand	132-133	2	11
β-strand	134	1	10
β-strand	137	1	10
β-strand	155-161	7	10
β-strand	170-176	7	10

Chain E: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	13
β-strand	10-14	5	9
β-strand	19-24	6	13
α-helix	25-26	2
β-strand	31-38	8	9
β-strand	42-50	9	9
β-strand	53-56	4	9
β-strand	65-71	7	13
β-strand	74-79	6	13
α-helix	84-86	3
β-strand	88-95	8	9
α-helix	97-100	4
β-strand	106-107	2	9
β-strand	111-116	6	9
α-helix	119-121	3
β-strand	123	1	14
α-helix	124-125	2
β-strand	126-130	5	12
α-helix	134-140	7
β-strand	142-152	11	12
β-strand	153	1	14
β-strand	157-163	7	15
β-strand	166-167	2	15
β-strand	172-174	3	12
α-helix	178	1
β-strand	179-180	2	12
β-strand	190-199	10	12
β-strand	209-216	8	15
β-strand	219	1	16
α-helix	230-231	2
β-strand	233	1	16
β-strand	235-242	8	15

Chain F: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	17
β-strand	21-28	8	17
β-strand	31-37	7	17
β-strand	46-47	2	17
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	17
β-strand	109-118	10	17
β-strand	121-126	6	17
β-strand	133-135	3	17
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	18
α-helix	184-185	2
β-strand	186-193	8	19
β-strand	198-208	11	19
β-strand	209	1	18
β-strand	214-219	6	20
β-strand	222-223	2	20
β-strand	228-230	3	19
α-helix	231-233	3
β-strand	234-235	2	19
β-strand	241-250	10	19
β-strand	257-262	6	20
β-strand	270-272	3	20

Chain I: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	24
β-strand	11-14	4	25
β-strand	19-25	7	24
β-strand	32-38	7	25
β-strand	44-51	8	25
β-strand	54-58	5	24
β-strand	61-66	6	24
β-strand	71-76	6	24
α-helix	81-83	3
β-strand	85-92	8	25
β-strand	100-101	2	25
β-strand	105-110	6	25
α-helix	111-112	2
β-strand	119-124	6	26
β-strand	132-137	6	26
β-strand	154-155	2	26
α-helix	156-158	3
β-strand	159-163	5	26
α-helix	164-166	3
β-strand	168-177	10	26
β-strand	198	1	26

Chain J: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	27
β-strand	10-14	5	25
β-strand	19-24	6	27
β-strand	31-38	8	25
β-strand	42-50	9	25
β-strand	53-56	4	25
β-strand	65-71	7	27
β-strand	74-79	6	27
α-helix	84-86	3
β-strand	88-95	8	25
α-helix	97-100	4
β-strand	106-107	2	25
β-strand	111-116	6	25
α-helix	119-121	3
β-strand	123	1	28
α-helix	124-125	2
β-strand	126-130	5	29
β-strand	131	1	26
α-helix	132-133	2
α-helix	134-140	7
β-strand	142-152	11	29
β-strand	153	1	28
β-strand	157-163	7	30
β-strand	166-168	3	30
β-strand	172-174	3	29
β-strand	179-180	2	29
β-strand	190-199	10	29
α-helix	200-204	5
β-strand	209-216	8	30
β-strand	219	1	31
α-helix	230-231	2
β-strand	233	1	31
β-strand	235-242	8	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, A-2 alpha chain	A, F	protein	277	Homo sapiens	P04439 (AlphaFold model)
Beta-2-microglobulin	B, G	protein	100	Homo sapiens	P61769 (AlphaFold model)
Marker peptide	C, H	protein	10	Homo sapiens
1E6 TCR Alpha Chain	D, I	protein	199	Homo sapiens	A0A0B4J271 (AlphaFold model), P01848 (AlphaFold model)
1E6 TCR Beta Chain	E, J	protein	246	Homo sapiens	A0A0B4J2E0, A0A5B9

Sequence of entity 1 (A, F), FASTA

>5C07_1 HLA class I histocompatibility antigen, A-2 alpha chain (chains A, F)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 2 (B, G), FASTA

>5C07_2 Beta-2-microglobulin (chains B, G)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H), FASTA

>5C07_3 Marker peptide (chains C, H)
YQFGPDFPIA

Sequence of entity 4 (D, I), FASTA

>5C07_4 1E6 TCR Alpha Chain (chains D, I)
KEVEQDPGPLSVPEGAIVSLNCTYSNSAFQYFMWYRQYSRKGPELLMYTYSSGNKEDGRF
TAQVDKSSKYISLFIRDSQPSDSATYLCAMRGDSSYKLIFGSGTRLLVRPDIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFP

Sequence of entity 5 (E, J), FASTA

>5C07_5 1E6 TCR Beta Chain (chains E, J)
DAGVIQSPRHEVTEMGQQVTLRCKPISGHDYLFWYRQTMMRGLELLIYFNNNVPIDDSGM
PEDRFSAKMPNASFSTLKIQPSEPRDSAVYFCASSLWEKLAKNIQYFGAGTRLSVLEDLK
NVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLK
EQPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAE
AWGRAD

Primary citation

Hotspot autoimmune T cell receptor binding underlies pathogen and insulin peptide cross-reactivity. Cole, D.K., Bulek, A.M., Dolton, G. et al. J Clin Invest (2016) 126:2191-2204. DOI 10.1172/JCI85679 · 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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