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- PDB-9hi7: Structure of MC.7.G5 T cell receptor in complex with MR1 R9H -

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Basic information

Entry
Database: PDB / ID: 9hi7
TitleStructure of MC.7.G5 T cell receptor in complex with MR1 R9H
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I-related gene protein
  • T cell receptor alpha chain MC.7.G5
  • T cell receptor beta chain MC.7.G5
KeywordsIMMUNE SYSTEM / TCR / MR1 / MAIT
Function / homology
Function and homology information


detection of tumor cell / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : ...detection of tumor cell / positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / alpha-beta T cell receptor complex / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of peptide antigen via MHC class I / beta-2-microglobulin binding / T cell receptor binding / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / signaling receptor activity / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / : / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin V-Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T cell receptor alpha chain MC.7.G5 / T cell receptor beta chain MC.7.G5 / Beta-2-microglobulin / Major histocompatibility complex class I-related gene protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsKaruppiah, V.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Front Immunol / Year: 2025
Title: Molecular basis underpinning MR1 allomorph recognition by an MR1-restricted T cell receptor.
Authors: Suckling, R.J. / Pamukcu, C. / Simmons, R.A. / Fonseca, D. / Grant, E. / Harrison, R. / Shaikh, S.A. / Khanolkar, R.C. / Ghadbane, H. / Creese, A. / Hock, M. / Gligoris, T.G. / Lepore, M. / ...Authors: Suckling, R.J. / Pamukcu, C. / Simmons, R.A. / Fonseca, D. / Grant, E. / Harrison, R. / Shaikh, S.A. / Khanolkar, R.C. / Ghadbane, H. / Creese, A. / Hock, M. / Gligoris, T.G. / Lepore, M. / Karuppiah, V. / Salio, M.
History
DepositionNov 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
D: T cell receptor alpha chain MC.7.G5
E: T cell receptor beta chain MC.7.G5
F: Major histocompatibility complex class I-related gene protein
G: Beta-2-microglobulin
H: T cell receptor alpha chain MC.7.G5
I: T cell receptor beta chain MC.7.G5


Theoretical massNumber of molelcules
Total (without water)193,0198
Polymers193,0198
Non-polymers00
Water362
1
A: Major histocompatibility complex class I-related gene protein
B: Beta-2-microglobulin
D: T cell receptor alpha chain MC.7.G5
E: T cell receptor beta chain MC.7.G5


Theoretical massNumber of molelcules
Total (without water)96,5104
Polymers96,5104
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Major histocompatibility complex class I-related gene protein
G: Beta-2-microglobulin
H: T cell receptor alpha chain MC.7.G5
I: T cell receptor beta chain MC.7.G5


Theoretical massNumber of molelcules
Total (without water)96,5104
Polymers96,5104
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.030, 113.202, 130.363
Angle α, β, γ (deg.)90.00, 90.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Major histocompatibility complex class I-related gene protein / MHC class I-related gene protein / Class I histocompatibility antigen-like protein


Mass: 33763.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q95460
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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
#3: Protein T cell receptor alpha chain MC.7.G5 / MC.7.G5 TRA / TR alpha chain TRAV38-2DV8*01J31*01C*01


Mass: 22690.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTU3
#4: Protein T cell receptor beta chain MC.7.G5 / TR beta chain TRBV25-1*01J2S3*01C2*01 / MC.7.G5 TRB


Mass: 28176.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRB / Production host: Escherichia coli (E. coli) / References: UniProt: P0DTU4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50 mM HEPES pH 7.0, 250 mM NaCl and 11% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.81→130.35 Å / Num. obs: 51269 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.207 / Rpim(I) all: 0.085 / Rrim(I) all: 0.225 / Net I/σ(I): 7.1
Reflection shellResolution: 2.81→2.879 Å / Redundancy: 6.7 % / Rmerge(I) obs: 3.03 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2548 / CC1/2: 0.382 / Rpim(I) all: 1.264 / Rrim(I) all: 3.287 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→130.35 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.889 / SU B: 64.237 / SU ML: 0.502 / Cross valid method: THROUGHOUT / ESU R: 0.791 / ESU R Free: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29576 2463 4.8 %RANDOM
Rwork0.23576 ---
obs0.23864 48599 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.573 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å2-0.3 Å2
2---3.55 Å2-0 Å2
3---0.83 Å2
Refinement stepCycle: 1 / Resolution: 2.81→130.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13005 0 0 2 13007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01213380
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612023
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.66718159
X-RAY DIFFRACTIONr_angle_other_deg0.6041.58527744
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.83751594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.544576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.776102216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.21927
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023223
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.879 Å
RfactorNum. reflection% reflection
Rfree0.406 168 -
Rwork0.384 3477 -
obs--96.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2253-0.11360.0473.0242-1.33861.61720.070.28920.36030.0862-0.01680.0042-0.3460.2288-0.05320.5672-0.0991-0.10140.12140.08860.149833.461270.293345.7104
21.5078-0.5145-0.90512.79481.08231.77620.0020.00740.51560.4816-0.11460.2835-0.1937-0.31520.11260.8972-0.0441-0.18990.1045-0.05750.403631.005188.338554.709
30.79231.23870.19395.0907-1.14971.86840.06050.0759-0.1167-0.23280.02910.21630.1733-0.2188-0.08960.38810.0133-0.16120.0771-0.05220.116411.359719.70450.6083
40.71141.1075-0.0653.777-0.38991.08320.1147-0.08130.11560.16030.07060.59980.0051-0.3307-0.18530.3241-0.0176-0.08050.12120.06140.14648.73625.155169.0258
51.7556-0.81640.35713.2734-0.61531.5145-0.124-0.1009-0.30770.08490.0715-0.20010.1530.22470.05250.56740.0021-0.10720.06460.03450.131115.4317-8.721413.1637
62.3149-0.5512-0.11295.0654-1.1561.184-0.0721-0.1072-0.4468-0.126-0.0740.19480.3158-0.010.1460.5466-0.0056-0.12740.11330.04110.22265.7822-26.442911.9873
71.1331-1.08290.34233.57220.48171.36730.0297-0.00850.13830.05880.0413-0.22410.1192-0.0389-0.0710.4561-0.0195-0.10980.08550.01280.05181.388543.260127.9417
80.6847-1.1497-0.00382.42070.4110.4109-0.037-0.0962-0.23370.2804-0.05360.46730.1271-0.24070.09050.6268-0.0207-0.07880.1612-0.02650.123-15.955537.467321.6372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 269
2X-RAY DIFFRACTION2B0 - 97
3X-RAY DIFFRACTION3D7 - 199
4X-RAY DIFFRACTION4E3 - 247
5X-RAY DIFFRACTION5F0 - 269
6X-RAY DIFFRACTION6G0 - 97
7X-RAY DIFFRACTION7H7 - 200
8X-RAY DIFFRACTION8I2 - 247

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