6ZKZ: InhA:01 TCR

Crystal structure of InhA:01 TCR in complex with HLA-E (F116C) bound to InhA (53-61 H4C). Determined by X-ray diffraction at 2.3 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Mycobacterium tuberculosis H37Rv
Chains: 5
Atoms: 6,582
Mol. weight: 93.91 kDa
Released: 26 Jan 2022

Explore 6ZKZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ZKZ contains 24 α-helices and 72 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: 11 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	57-84	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	138-140	3
α-helix	141-149	9
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-173	10
α-helix	176-179	4
β-strand	183	1	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	229-230	2	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

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
α-helix	46	1
β-strand	50-51	2	6
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	4-7	4	8
β-strand	10-14	5	9
β-strand	19-25	7	8
β-strand	38-44	7	9
β-strand	50-57	8	9
β-strand	65-68	4	8
β-strand	76-81	6	8
β-strand	86-91	6	8
α-helix	96-98	3
β-strand	100-107	8	9
β-strand	116-118	3	9
β-strand	122-127	6	9
β-strand	136-141	6	10
β-strand	142	1	11
β-strand	149-154	6	10
α-helix	160-164	5
β-strand	170-172	3	10
α-helix	173-175	3
β-strand	176-180	5	10
α-helix	181-183	3
β-strand	185-194	10	10

Chain E: 7 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-21	3	14
β-strand	22-25	4	12
β-strand	38-45	8	13
β-strand	49-58	10	13
β-strand	65-68	4	13
β-strand	76-78	3	14
β-strand	86	1	12
β-strand	89-91	3	14
α-helix	96-98	3
β-strand	100-107	8	13
β-strand	117-118	2	13
β-strand	122-127	6	13
α-helix	130-132	3
β-strand	134	1	15
α-helix	135-136	2
β-strand	137-141	5	11
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	11
β-strand	164	1	15
β-strand	168-174	7	16
β-strand	177-179	3	16
β-strand	183-185	3	11
α-helix	189	1
β-strand	190-191	2	11
β-strand	201-210	10	11
α-helix	211-215	5
β-strand	220-227	8	16
β-strand	230	1	17
β-strand	244	1	17
β-strand	246-253	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A	protein	276	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Enoyl-[acyl-carrier-protein] reductase [NADH]	C	protein	9	Mycobacterium tuberculosis H37Rv	P9WGR1 (AlphaFold model)
T-cell receptor alpha chain	D	protein	199	Homo sapiens
T-cell receptor beta chain	E	protein	245	Homo sapiens

Sequence of entity 1 (A), FASTA

>6ZKZ_1 HLA class I histocompatibility antigen, alpha chain E (chains A)
GSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEYW
DRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQCAYDG
KDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETLL
HLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDGT
FQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (B), FASTA

>6ZKZ_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6ZKZ_3 Enoyl-[acyl-carrier-protein] reductase [NADH] (chains C)
RLPAKAPLL

Sequence of entity 4 (D), FASTA

>6ZKZ_4 T-cell receptor alpha chain (chains D)
MAQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSSNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDT

Sequence of entity 5 (E), FASTA

>6ZKZ_5 T-cell receptor beta chain (chains E)
NAGVTQTPKFQVLKTGQSMTLQCSQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGEV
PNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYSIRGSRGEQFFGPGTRLTVLEDLKN
VFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRAD

Primary citation

Structure-guided stabilization of pathogen-derived peptide-HLA-E complexes using non-natural amino acids conserves native TCR recognition. Barber, C., De Souza, V.A., Paterson, R.L. et al. Eur J Immunol (2022) 52:618-632. DOI 10.1002/eji.202149745 · 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)
9NW8 2.3 Å, CA117v2v8 Fab bound to HLA-E-Mtb44
9NW9 2.3 Å, CA117v2v8 Fab bound to HLA-E-RL9HIV
8QFY 2.33 Å, Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide

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