PDB-8qfy: Crystal structure of high affinity TCR in complex with pHLA harbo...

ID or keywords:

Entry

Database: PDB / ID: 8qfy

Title

Crystal structure of high affinity TCR in complex with pHLA harbouring bacterial peptide

Components

(T-cell receptor ...) x 2
Beta-2-microglobulinBeta-2 microglobulin
HLA class I histocompatibility antigen, alpha chain E
Peptide from inhA

Keywords

IMMUNE SYSTEM /

T-cell receptor /

HLA-E

Function / homology

Function and homology information

positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / positive regulation of immunoglobulin production / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / positive regulation of interleukin-4 production / MHC class I protein binding /

protection from natural killer cell mediated cytotoxicity /

beta-2-microglobulin binding /

T cell receptor binding / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane /

regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis /

adaptive immune response / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium /

immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane /

endoplasmic reticulum lumen /

Golgi membrane /

signaling receptor binding /

focal adhesion
Similarity search - Function

Biological species

Homo sapiens (human)

Mycobacterium tuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.33 Å

Authors

Pengelly, R.J. / Robinson, R.A.

Funding support

1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: An HLA-E-targeted TCR bispecific molecule redirects T cell immunity against Mycobacterium tuberculosis.
Authors: Paterson, R.L. / La Manna, M.P. / Arena De Souza, V. / Walker, A. / Gibbs-Howe, D. / Kulkarni, R. / Fergusson, J.R. / Mulakkal, N.C. / Monteiro, M. / Bunjobpol, W. / Dembek, M. / Martin- ...

History

Deposition	Sep 5, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8qfy.cif.gz	350.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8qfy.ent.gz		Display	PDB format
PDBx/mmJSON format	8qfy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qf/8qfy ftp://data.pdbj.org/pub/pdb/validation_reports/qf/8qfy	HTTPS FTP

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Related structure data

Related structure data	4ww2S 6gh1S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#62 - Feb 2005 Major Histocompatibility Complex similarity (3) #63 - Mar 2005 T-Cell Receptor similarity (4)

Deposited unit

AAA: HLA class I histocompatibility antigen, alpha chain E

BBB: Beta-2-microglobulin

CCC: Peptide from inhA

DDD: T-cell receptor alpha chain

EEE: T-cell receptor beta chain

FFF: HLA class I histocompatibility antigen, alpha chain E

GGG: Beta-2-microglobulin

HHH: Peptide from inhA

III: T-cell receptor alpha chain

JJJ: T-cell receptor beta chain

hetero molecules

189 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: HLA class I histocompatibility antigen, alpha chain E

BBB: Beta-2-microglobulin

CCC: Peptide from inhA

DDD: T-cell receptor alpha chain

EEE: T-cell receptor beta chain

defined by author
Evidence: gel filtration
94.5 kDa, 5 polymers

2

FFF: HLA class I histocompatibility antigen, alpha chain E

GGG: Beta-2-microglobulin

HHH: Peptide from inhA

III: T-cell receptor alpha chain

JJJ: T-cell receptor beta chain

hetero molecules

defined by author
94.6 kDa, 5 polymers

Unit cell

Length a, b, c (Å)	326.828, 79.879, 104.073
Angle α, β, γ (deg.)	90.000, 96.894, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	FFF
3	2	BBB
4	2	GGG
5	3	DDD
6	3	III
7	4	EEE
8	4	JJJ

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	GLY	GLY	THR	THR	AAA	A	1 - 271	1 - 271
2	2	1	GLY	GLY	THR	THR	FFF	F	1 - 271	1 - 271
3	3	2	MET	MET	MET	MET	BBB	B	0 - 99	1 - 100
4	4	2	MET	MET	MET	MET	GGG	G	0 - 99	1 - 100
5	5	3	LYS	LYS	ASN	ASN	DDD	D	3 - 189	3 - 189
6	6	3	LYS	LYS	ASN	ASN	III	I	3 - 189	3 - 189
7	7	4	THR	THR	ASP	ASP	EEE	E	3 - 243	3 - 243
8	8	4	THR	THR	ASP	ASP	JJJ	J	3 - 243	3 - 243

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8

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Protein , 2 types, 4 molecules AAAFFFBBBGGG

#1: Protein	HLA class I histocompatibility antigen, alpha chain E / MHC class I antigen E Mass: 31824.008 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-E, HLA-6.2, HLAE / Production host: Escherichia coli (E. coli) / References: UniProt: P13747
#2: Protein	Beta-2-microglobulin / Beta-2 microglobulin Mass: 11879.356 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 2 molecules CCCHHH

#3: Protein/peptide	Peptide from inhA / Mass: 980.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mycobacterium tuberculosis (bacteria)

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T-cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ

#4: Protein	T-cell receptor alpha chain Mass: 22079.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein	T-cell receptor beta chain Mass: 27693.766 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 283 molecules

#6: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.57 Å³/Da / Density % sol: 65.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 0.2 M calcium acetate, 0.1 M imidazole pH 8.0, 10% PEG 8000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 24, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.33→82.9 Å / Num. obs: 114168 / % possible obs: 100 % / Redundancy: 6.8 % / CC_1/2: 0.987 / R_merge(I) obs: 0.121 / R_rim(I) all: 0.131 / Net I/σ(I): 11.3
Reflection shell	Resolution: 2.33→2.37 Å / Redundancy: 6 % / R_merge(I) obs: 3.209 / Num. unique obs: 5720 / CC_1/2: 0.34 / R_rim(I) all: 3.521 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
DIALS	3.1.2	data reduction
DIALS	3.1.2	data scaling
PHASER	2.8.3	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6GH1, 4WW2

6gh1

4ww2

Resolution: 2.33→82.9 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.921 / WR_factor R_free: 0.253 / WR_factor R_work: 0.206 / SU B: 15.989 / SU ML: 0.323 / Average fsc free: 0.6939 / Average fsc work: 0.7064 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.238
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2886	5685	4.981 %
R_work	0.2425	108459	-
all	0.245	-	-
obs	-	114144	99.947 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 74.978 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.741 Å²	0 Å²	-2.502 Å²
2-	-	6.869 Å²	0 Å²
3-	-	-	-3.423 Å²

Refinement step

Cycle: LAST / Resolution: 2.33→82.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12837	0	8	281	13126

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	13218
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	11866
X-RAY DIFFRACTION	r_angle_refined_deg	1.406	1.652	17946
X-RAY DIFFRACTION	r_angle_other_deg	1.153	1.583	27379
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.377	5	1586
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.324	21.828	793
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.572	15	2164
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.089	15	107
X-RAY DIFFRACTION	r_chiral_restr	0.053	0.2	1653
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	15161
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3245
X-RAY DIFFRACTION	r_nbd_refined	0.199	0.2	2262
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.191	0.2	10749
X-RAY DIFFRACTION	r_nbtor_refined	0.164	0.2	5908
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.076	0.2	6500
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	347
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.134	0.2	6
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.286	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.264	0.2	80
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.208	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	5.649	7.814	6367
X-RAY DIFFRACTION	r_mcbond_other	5.65	7.813	6365
X-RAY DIFFRACTION	r_mcangle_it	8.545	11.703	7938
X-RAY DIFFRACTION	r_mcangle_other	8.544	11.704	7939
X-RAY DIFFRACTION	r_scbond_it	5.272	8.217	6851
X-RAY DIFFRACTION	r_scbond_other	5.271	8.217	6852
X-RAY DIFFRACTION	r_scangle_it	8.322	12.172	10006
X-RAY DIFFRACTION	r_scangle_other	8.322	12.172	10007
X-RAY DIFFRACTION	r_lrange_it	12.213	86.122	13827
X-RAY DIFFRACTION	r_lrange_other	12.213	86.125	13828
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.082	0.05	7792
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.035	0.05	3056
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.091	0.05	5476
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.066	0.05	7526

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.08175	0.05009
1	2	FFF	X-RAY DIFFRACTION	Local ncs	0.08175	0.05009
2	3	BBB	X-RAY DIFFRACTION	Local ncs	0.03456	0.0501
2	4	GGG	X-RAY DIFFRACTION	Local ncs	0.03456	0.0501
3	5	DDD	X-RAY DIFFRACTION	Local ncs	0.09093	0.0501
3	6	III	X-RAY DIFFRACTION	Local ncs	0.09093	0.0501
4	7	EEE	X-RAY DIFFRACTION	Local ncs	0.06607	0.05009
4	8	JJJ	X-RAY DIFFRACTION	Local ncs	0.06607	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.33-2.39	0.433	400	0.434	7969	X-RAY DIFFRACTION	99.5835
2.39-2.455	0.41	421	0.405	7744	X-RAY DIFFRACTION	100
2.455-2.527	0.415	384	0.395	7597	X-RAY DIFFRACTION	99.9875
2.527-2.604	0.405	398	0.382	7337	X-RAY DIFFRACTION	99.9225
2.604-2.69	0.406	354	0.38	7136	X-RAY DIFFRACTION	99.96
2.69-2.784	0.388	376	0.356	6859	X-RAY DIFFRACTION	99.9171
2.784-2.889	0.34	350	0.322	6670	X-RAY DIFFRACTION	99.9715
2.889-3.007	0.311	312	0.298	6438	X-RAY DIFFRACTION	99.9704
3.007-3.141	0.323	340	0.267	6128	X-RAY DIFFRACTION	99.9845
3.141-3.294	0.263	331	0.238	5862	X-RAY DIFFRACTION	100
3.294-3.472	0.284	329	0.237	5601	X-RAY DIFFRACTION	99.9831
3.472-3.683	0.298	268	0.232	5266	X-RAY DIFFRACTION	100
3.683-3.937	0.273	270	0.219	4981	X-RAY DIFFRACTION	100
3.937-4.252	0.253	228	0.194	4687	X-RAY DIFFRACTION	99.9797
4.252-4.658	0.206	224	0.165	4300	X-RAY DIFFRACTION	100
4.658-5.207	0.224	199	0.168	3899	X-RAY DIFFRACTION	100
5.207-6.011	0.271	164	0.19	3457	X-RAY DIFFRACTION	100
6.011-7.36	0.328	158	0.212	2921	X-RAY DIFFRACTION	100
7.36-10.398	0.206	113	0.178	2303	X-RAY DIFFRACTION	100
10.398-82.9	0.303	66	0.293	1305	X-RAY DIFFRACTION	99.7817

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Protein , 2 types, 4 molecules AAAFFFBBBGGG

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Protein/peptide , 1 types, 2 molecules CCCHHH

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T-cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ

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Non-polymers , 2 types, 283 molecules

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-Protein , 2 types, 4 molecules AAAFFFBBBGGG

-Protein/peptide , 1 types, 2 molecules CCCHHH

-T-cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ

-Non-polymers , 2 types, 283 molecules

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Protein , 2 types, 4 molecules AAAFFFBBBGGG

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Protein/peptide , 1 types, 2 molecules CCCHHH

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T-cell receptor ... , 2 types, 4 molecules DDDIIIEEEJJJ

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Non-polymers , 2 types, 283 molecules

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