8QFY: High affinity TCR

Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide. Determined by X-ray diffraction at 2.33 Å resolution. Released 15 May 2024.

Method: X-ray diffraction
Resolution: 2.33 Å
Organisms: Homo sapiens, Mycobacterium tuberculosis
Chains: 10
Atoms: 13,151
Mol. weight: 189.03 kDa
Released: 15 May 2024

Explore 8QFY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8QFY contains 54 α-helices and 141 β-strands across 9 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 AAA: 9 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	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	50-52	3
α-helix	57-85	29
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	139-150	12
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
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-215	2	4
β-strand	230	1	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-246	6	3
β-strand	261-262	2	4
β-strand	270	1	4

Chains BBB and GGG: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6	1	6
α-helix	7	1
β-strand	9-11	3	7
α-helix	14-15	2
β-strand	21-30	10	7
β-strand	31	1	5
β-strand	35-41	7	8
β-strand	44-45	2	8
α-helix	46	1
β-strand	50-51	2	7
α-helix	52-54	3
β-strand	55-56	2	7
β-strand	62-70	9	7
β-strand	78-84	7	8
β-strand	91-94	4	8

Chain DDD: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	9
β-strand	12-15	4	10
α-helix	19	1
β-strand	20-26	7	9
β-strand	33-39	7	10
β-strand	46-51	6	10
β-strand	55-59	5	9
β-strand	62-67	6	9
β-strand	72-77	6	9
α-helix	82-84	3
β-strand	86-93	8	10
β-strand	99-101	3	10
β-strand	105-110	6	10
β-strand	119-124	6	11
β-strand	125	1	12
β-strand	132-137	6	11
β-strand	154-155	2	11
α-helix	156-158	3
β-strand	159-163	5	11
α-helix	164-166	3
β-strand	168-176	9	11

Chain EEE: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	13
β-strand	11-15	5	14
β-strand	20-25	6	13
β-strand	32-38	7	14
β-strand	45-51	7	14
β-strand	54-58	5	14
β-strand	66-69	4	13
β-strand	76-80	5	13
α-helix	85-87	3
β-strand	89-96	8	14
β-strand	103-104	2	14
β-strand	108-113	6	14
α-helix	116-118	3
β-strand	120	1	15
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	15
β-strand	154-160	7	16
β-strand	163-165	3	16
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	16
β-strand	216	1	17
α-helix	227-228	2
β-strand	230	1	17
β-strand	232-239	8	16

Chain FFF: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	18
α-helix	20	1
β-strand	21-28	8	18
β-strand	31-37	7	18
β-strand	45-47	3	18
α-helix	50-52	3
α-helix	57-85	29
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	139-149	11
α-helix	152-158	7
α-helix	159-163	5
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	199-208	10	20
β-strand	209	1	19
β-strand	214-217	4	21
β-strand	229-230	2	20
α-helix	231-233	3
β-strand	234-235	2	20
β-strand	241-246	6	20
β-strand	259-262	4	21
β-strand	270-272	3	21

Chain HHH: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	6-8	3

Chain III: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	26
β-strand	12-15	4	27
α-helix	19	1
β-strand	20-26	7	26
β-strand	33-39	7	27
α-helix	44-45	2
β-strand	46-51	6	27
β-strand	55-59	5	26
β-strand	62-67	6	26
β-strand	72-77	6	26
α-helix	82-84	3
β-strand	86-93	8	27
β-strand	99-101	3	27
β-strand	105-110	6	27
β-strand	119-125	7	28
β-strand	132-137	6	28
β-strand	154-155	2	28
α-helix	156-158	3
β-strand	159-163	5	28
α-helix	164-166	3
β-strand	168-176	9	28

Chain JJJ: 8 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	6-8	3	29
β-strand	11-15	5	30
β-strand	20-25	6	29
β-strand	32-38	7	30
β-strand	45-51	7	30
β-strand	54-58	5	30
β-strand	66-69	4	29
β-strand	76-80	5	29
α-helix	85-87	3
β-strand	89-96	8	30
β-strand	103-104	2	30
α-helix	105	1
β-strand	108-113	6	30
α-helix	116-118	3
β-strand	120	1	31
α-helix	121-122	2
β-strand	123-128	6	28
α-helix	129-130	2
α-helix	131-137	7
β-strand	139-149	11	28
β-strand	150	1	31
β-strand	154-160	7	32
β-strand	163-165	3	32
β-strand	169-171	3	28
β-strand	176-177	2	28
β-strand	187-196	10	28
α-helix	197-201	5
β-strand	206-213	8	32
β-strand	216	1	33
α-helix	227-228	2
β-strand	230	1	33
β-strand	232-239	8	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	AAA, FFF	protein	276	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	BBB, GGG	protein	100	Homo sapiens	P61769 (AlphaFold model)
Peptide from inhA	CCC, HHH	protein	9	Mycobacterium tuberculosis	P9WGR1 (AlphaFold model)
T-cell receptor alpha chain	DDD, III	protein	197	Homo sapiens
T-cell receptor beta chain	EEE, JJJ	protein	243	Homo sapiens

Sequence of entity 1 (AAA, FFF), FASTA

>8QFY_1 HLA class I histocompatibility antigen, alpha chain E (chains AAA, FFF)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (BBB, GGG), FASTA

>8QFY_2 Beta-2-microglobulin (chains BBB, GGG)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (CCC, HHH), FASTA

>8QFY_3 Peptide from inhA (chains CCC, HHH)
RLPAKAPLL

Sequence of entity 4 (DDD, III), FASTA

>8QFY_4 T-cell receptor alpha chain (chains DDD, III)
MAKEVEQNSGPLSVPEGAIASLNCTYSDRRSRSFFWYRQYSGKSPELIMSIYSNGDKEDG
RFTAQLNKASQYVSLLIRDSQPSDSATYLCAVMDREYEISFGSGTRLLVRPDIQNPDPAV
YQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKS
DFACANAFNNSIIPEDT

Sequence of entity 5 (EEE, JJJ), FASTA

>8QFY_5 T-cell receptor beta chain (chains EEE, JJJ)
MDTGVSQNPRHKITKRGQNVTFRCDPISDHNRLYWYRQTLGQGPEFLTYFQSEAQLEKSR
LLSDRFSAERPKGSFSTLEIQRTEQGDSAMYLCASSLGPNEQLFGPGTRLTVVEDLNKVF
PPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQP
ALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWG
RAD

Primary citation

An HLA-E-targeted TCR bispecific molecule redirects T cell immunity against Mycobacterium tuberculosis. Paterson, R.L., La Manna, M.P., Arena De Souza, V. et al. Proc Natl Acad Sci U S A (2024) 121:e2318003121-e2318003121. DOI 10.1073/pnas.2318003121 · PubMed

Other PDB entries of the same protein (UniProt P13747 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7P4B 1.72 Å, HLA-E*01:03 in complex with IL9
7BH8 1.8 Å, 3H4-Fab HLA-E-VL9 co-complex
7P49 2.05 Å, HLA-E*01:03 in complex with Mtb14
6GH1 2.1 Å, HLA-E*01:03 in complex with Mtb44
9NW7 2.1 Å, CA117v2v8 Fab bound to HLA-E-VL9
6GH4 2.16 Å, HLA-E*01:03 in complex with the Mtb44 peptide variant: Mtb44*P2-Gln.
6ZKX 2.17 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG)
8RLT 2.25 Å, TCR in complex with HLA-E*01:03 bound to HBV envelope 371-379 index peptide
6ZKW 2.26 Å, Crystal structure of InhA:01 TCR in complex with HLA-E bound to InhA (53-61)
6ZKZ 2.3 Å, Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV

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