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- PDB-6mwr: Recognition of MHC-like molecule -

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Basic information

Entry
Database: PDB / ID: 6mwr
TitleRecognition of MHC-like molecule
Components
  • Beta-2-microglobulin
  • Delta chain of T cell receptor
  • G7 Gamma chain T cell receptor
  • Major histocompatibility complex class I-related gene protein
KeywordsIMMUNE SYSTEM / MHC-like molecule
Function / homology
Function and homology information


positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway ...positive regulation of T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of exogenous antigen / MHC class I receptor activity / beta-2-microglobulin binding / antigen processing and presentation of peptide antigen via MHC class I / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / T cell mediated cytotoxicity / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / Interferon gamma signaling / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / immune response / defense response to Gram-positive bacterium / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / innate immune response / lysosomal membrane / 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
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-2LJ / Beta-2-microglobulin / Major histocompatibility complex class I-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsLe Nours, J. / Rossjohn, J.
CitationJournal: Science / Year: 2019
Title: A class of gamma delta T cell receptors recognize the underside of the antigen-presenting molecule MR1.
Authors: Le Nours, J. / Gherardin, N.A. / Ramarathinam, S.H. / Awad, W. / Wiede, F. / Gully, B.S. / Khandokar, Y. / Praveena, T. / Wubben, J.M. / Sandow, J.J. / Webb, A.I. / von Borstel, A. / Rice, M. ...Authors: Le Nours, J. / Gherardin, N.A. / Ramarathinam, S.H. / Awad, W. / Wiede, F. / Gully, B.S. / Khandokar, Y. / Praveena, T. / Wubben, J.M. / Sandow, J.J. / Webb, A.I. / von Borstel, A. / Rice, M.T. / Redmond, S.J. / Seneviratna, R. / Sandoval-Romero, M.L. / Li, S. / Souter, M.N.T. / Eckle, S.B.G. / Corbett, A.J. / Reid, H.H. / Liu, L. / Fairlie, D.P. / Giles, E.M. / Westall, G.P. / Tothill, R.W. / Davey, M.S. / Berry, R. / Tiganis, T. / McCluskey, J. / Pellicci, D.G. / Purcell, A.W. / Uldrich, A.P. / Godfrey, D.I. / Rossjohn, J.
History
DepositionOct 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: G7 Gamma chain T cell receptor
D: Delta chain of T cell receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1396
Polymers97,6024
Non-polymers5382
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-49 kcal/mol
Surface area38260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.390, 88.390, 257.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 4 types, 4 molecules ABCD

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


Mass: 31711.670 Da / Num. of mol.: 1
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: 11748.160 Da / Num. of mol.: 1
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 G7 Gamma chain T cell receptor


Mass: 27589.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#4: Protein Delta chain of T cell receptor


Mass: 26552.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pHLSEC / Cell line (production host): 293S / Production host: Homo sapiens (human)

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Sugars , 1 types, 1 molecules

#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 3 molecules

#5: Chemical ChemComp-2LJ / 1-deoxy-1-({2,6-dioxo-5-[(E)-propylideneamino]-1,2,3,6-tetrahydropyrimidin-4-yl}amino)-D-ribitol / 5-(2-oxopropylideneamino)-6-D-ribitylaminouracil


Mass: 316.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H20N4O6
#7: Water ChemComp-HOH / water


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

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Details

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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15-17% PEG3350 0.2M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.3→88.39 Å / Num. obs: 16174 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 50.54 Å2 / Rpim(I) all: 0.119 / Net I/σ(I): 6.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2287 / Rpim(I) all: 0.456 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GUP, 1HXM, 4LFH

4gup

1hxm

4lfh


Resolution: 3.3→44.45 Å / Cor.coef. Fo:Fc: 0.838 / Cor.coef. Fo:Fc free: 0.836 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.52
RfactorNum. reflection% reflectionSelection details
Rfree0.261 802 4.98 %RANDOM
Rwork0.238 ---
obs0.239 16108 99.9 %-
Displacement parametersBiso mean: 83.32 Å2
Baniso -1Baniso -2Baniso -3
1-2.3088 Å20 Å20 Å2
2--2.3088 Å20 Å2
3----4.6176 Å2
Refine analyzeLuzzati coordinate error obs: 0.6 Å
Refinement stepCycle: 1 / Resolution: 3.3→44.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5932 0 36 2 5970
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076139HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.878425HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1897SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1052HARMONIC5
X-RAY DIFFRACTIONt_it6139HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.23
X-RAY DIFFRACTIONt_other_torsion22.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion851SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5907SEMIHARMONIC4
LS refinement shellResolution: 3.3→3.53 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2873 118 4.14 %
Rwork0.2582 2733 -
all0.2594 2851 -
obs--100 %
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)
13.4271-0.3263-2.9070.6275-0.16276.6053-0.0636-0.0722-0.0672-0.2648-0.1496-0.2471-0.27580.01170.21310.1122-0.1420.0519-0.187-0.1521-0.30351.980122.535545.7104
22.8198-1.06842.91751.47242.64015.11360.0052-0.18910.04060.01060.0027-0.24560.01910.0765-0.00790.1117-0.1522-0.12270.2209-0.0955-0.304711.173823.491463.4454
31.9514-0.48722.88323.6252-2.92434.976-0.01110.02710.4250.07060.05790.1380.0127-0.0484-0.04680.06580.1517-0.1524-0.0539-0.1366-0.2304-33.245352.815238.5236
40.5243-0.65420.34134.3169-2.90351.56740.08050.11910.29760.06480.1198-0.1626-0.00940.0555-0.20030.1592-0.0123-0.1417-0.0313-0.04540.0126-15.701755.017931.5163
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }

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