6ZKX: InhA:01 TCR

Crystal structure of InhA:01 TCR in complex with HLA-E (Y84C) bound to InhA (53-61 GCG). Determined by X-ray diffraction at 2.17 Å resolution. Released 26 Jan 2022.

Method: X-ray diffraction
Resolution: 2.17 Å
Organisms: Homo sapiens, Mycobacterium tuberculosis H37Rv
Chains: 5
Atoms: 6,828
Mol. weight: 94.46 kDa
Released: 26 Jan 2022

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

Secondary structure: helices and β-sheets

6ZKX contains 25 α-helices and 75 β-strands across 5 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, 20 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	45-47	3	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
β-strand	140-142	3	2
α-helix	149-158	10
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	3
α-helix	184-185	2
β-strand	186-193	8	4
β-strand	198-208	11	4
β-strand	209	1	3
β-strand	214-219	6	5
β-strand	225	1	5
α-helix	226-227	2
β-strand	229-230	2	4
β-strand	234-235	2	4
β-strand	241-250	10	4
α-helix	254-256	3
β-strand	257-262	6	5
β-strand	270-272	3	5

Chain B: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	6
α-helix	6-7	2
β-strand	8-13	6	7
β-strand	23-32	10	7
β-strand	33	1	6
β-strand	38-43	6	8
β-strand	46-47	2	8
α-helix	48	1
β-strand	52-53	2	7
α-helix	54-56	3
β-strand	57-58	2	7
β-strand	64-72	9	7
β-strand	80-85	6	8
β-strand	93-96	4	8

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	9-11	3	2

Chain D: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	9
β-strand	10-14	5	10
β-strand	19-25	7	9
β-strand	38-44	7	10
β-strand	50-57	8	10
β-strand	65-68	4	9
β-strand	76-81	6	9
β-strand	86-91	6	9
α-helix	96-98	3
β-strand	100-107	8	10
β-strand	116-118	3	10
β-strand	122-127	6	10
β-strand	136-141	6	11
β-strand	142	1	12
β-strand	149-154	6	11
α-helix	160-164	5
β-strand	170-172	3	11
α-helix	173-175	3
β-strand	176-180	5	11
α-helix	181-183	3
β-strand	185-194	10	11

Chain E: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	10-14	5	14
β-strand	19-21	3	15
β-strand	22-25	4	13
β-strand	38-45	8	14
β-strand	49-58	10	14
β-strand	65-68	4	14
β-strand	76-78	3	15
β-strand	86	1	13
β-strand	89-91	3	15
α-helix	96-98	3
β-strand	100-107	8	14
α-helix	115-116	2
β-strand	117-118	2	14
β-strand	122-127	6	14
α-helix	130-132	3
β-strand	134	1	16
α-helix	135-136	2
β-strand	137-141	5	12
α-helix	142-144	3
α-helix	145-151	7
β-strand	153-163	11	12
β-strand	164	1	16
β-strand	168-174	7	17
β-strand	177-178	2	17
β-strand	183-185	3	12
α-helix	189	1
β-strand	190-191	2	12
β-strand	201-210	10	12
α-helix	211-215	5
β-strand	220-227	8	17
β-strand	230	1	18
β-strand	244	1	18
β-strand	246-253	8	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen, alpha chain E	A	protein	277	Homo sapiens	P13747 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Enoyl-[acyl-carrier-protein] reductase [NADH]	C	protein	12	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

>6ZKX_1 HLA class I histocompatibility antigen, alpha chain E (chains A)
MGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDNDAASPRMVPRAPWMEQEGSEY
WDRETRSARDTAQIFRVNLRTLRGCYNQSEAGSHTLQWMHGCELGPDGRFLRGYEQFAYD
GKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAYLEDTCVEWLHKYLEKGKETL
LHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAGDG
TFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKP

Sequence of entity 2 (B), FASTA

>6ZKX_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>6ZKX_3 Enoyl-[acyl-carrier-protein] reductase [NADH] (chains C)
RLPAKAPLLGCG

Sequence of entity 4 (D), FASTA

>6ZKX_4 T-cell receptor alpha chain (chains D)
MAQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGRSTLYIAASQPGDSATYLCAVTNQAGTALIFGKGTTLSVSSNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDT

Sequence of entity 5 (E), FASTA

>6ZKX_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.
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
8QFY 2.33 Å, Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide

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