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- PDB-7q9a: MHC Class I A02 Allele presenting LLLGIGILVL, in complex with Mel5 TCR -

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Basic information

Entry
Database: PDB / ID: 7q9a
TitleMHC Class I A02 Allele presenting LLLGIGILVL, in complex with Mel5 TCR
Components
  • (Human Mel5 T Cell Receptor, ...) x 2
  • Beta-2-microglobulin
  • LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL-LEU
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / BST2 / Diabetes / Autoimmunity
Function / homology
Function and homology information


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 / 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 ...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 / 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 / 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 / negative regulation of forebrain neuron differentiation / MHC class II protein complex / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 receptor-mediated endocytosis / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / 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
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Wall, A. / Fuller, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2023
Title: Targeting of multiple tumor-associated antigens by individual T cell receptors during successful cancer immunotherapy.
Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. ...Authors: Dolton, G. / Rius, C. / Wall, A. / Szomolay, B. / Bianchi, V. / Galloway, S.A.E. / Hasan, M.S. / Morin, T. / Caillaud, M.E. / Thomas, H.L. / Theaker, S. / Tan, L.R. / Fuller, A. / Topley, K. / Legut, M. / Attaf, M. / Hopkins, J.R. / Behiry, E. / Zabkiewicz, J. / Alvares, C. / Lloyd, A. / Rogers, A. / Henley, P. / Fegan, C. / Ottmann, O. / Man, S. / Crowther, M.D. / Donia, M. / Svane, I.M. / Cole, D.K. / Brown, P.E. / Rizkallah, P. / Sewell, A.K.
History
DepositionNov 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL-LEU
D: Human Mel5 T Cell Receptor, Alpha Chain
E: Human Mel5 T Cell Receptor, Beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4349
Polymers94,0655
Non-polymers3684
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.019, 122.019, 82.418
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5B8RNS7
#2: Protein Beta-2-microglobulin


Mass: 11879.356 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide LEU-LEU-LEU-GLY-ILE-GLY-ILE-LEU-VAL-LEU


Mass: 1023.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Human Mel5 T Cell Receptor, ... , 2 types, 2 molecules DE

#4: Protein Human Mel5 T Cell Receptor, Alpha Chain


Mass: 21947.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein Human Mel5 T Cell Receptor, Beta Chain


Mass: 27264.367 Da / Num. of mol.: 1
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, 232 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.26 Å3/Da / Density % sol: 62.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M TRIS, 15% PEG 8000, 15% Glycerol, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.1→61.02 Å / Num. obs: 70731 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.04 / Rrim(I) all: 0.113 / Net I/σ(I): 10.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.8 % / Rmerge(I) obs: 2.6 / Num. unique obs: 3512 / CC1/2: 0.312 / Rpim(I) all: 0.989 / Rrim(I) all: 2.8 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
xia2data scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HG1

3hg1


Resolution: 2.1→61.01 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 16.744 / SU ML: 0.193 / SU R Cruickshank DPI: 0.1829 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.183 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2432 3454 4.9 %RANDOM
Rwork0.2045 ---
obs0.2064 67098 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.22 Å2 / Biso mean: 63.387 Å2 / Biso min: 33.68 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2---1 Å20 Å2
3---1.99 Å2
Refinement stepCycle: final / Resolution: 2.1→61.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6629 0 24 228 6881
Biso mean--80.23 56.53 -
Num. residues----829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136865
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156156
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.6479331
X-RAY DIFFRACTIONr_angle_other_deg1.2641.58114200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6025830
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95222.265393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.391151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7771547
X-RAY DIFFRACTIONr_chiral_restr0.0740.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027893
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021673
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 241 -
Rwork0.389 4792 -
all-5033 -
obs--97.11 %
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)
11.8330.0780.78943.115-0.94783.5932-0.106-0.06460.12650.05520.1322-0.1094-0.2063-0.1449-0.02620.10580.0033-0.01210.3132-0.00130.018454.69847.8055-4.8266
27.03012.5013-0.44341.0041-0.05240.2558-0.1486-0.00730.1723-0.10470.1753-0.214-0.16270.4659-0.02670.875-0.1635-0.21581.03590.09661.103778.548434.3370.1689
33.1578-1.09630.58315.40591.04954.2117-0.3569-0.41610.73240.45050.05640.0086-0.9987-0.18750.30050.4830.0346-0.09780.3894-0.08720.187264.381623.546915.2168
44.33911.44261.33282.52520.57922.6012-0.15190.2591-0.0438-0.16560.11970.096-0.06950.14710.03220.17010.00810.00060.28320.04690.015335.5745-2.3921-26.0243
56.5038-0.0758-1.94064.91940.48416.8504-0.03340.7859-0.006-0.45730.08440.30480.0375-0.7694-0.05090.7377-0.06560.01050.68580.02650.23147.1896-19.6376-37.1545
69.09691.3132-0.02781.2364-0.2281.35450.1627-0.4397-0.0410.2974-0.1780.08520.03120.02060.01530.2778-0.04250.00290.24830.03830.039228.8144-5.6856-3.7282
73.5253-0.3795-1.82053.42951.36976.267-0.14980.4237-0.1221-0.39760.0798-0.22390.2924-0.03740.06990.3283-0.0520.06670.26070.03280.16229.3814-23.455-20.5537
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 9
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B1 - 99
5X-RAY DIFFRACTION4D2 - 110
6X-RAY DIFFRACTION5D115 - 200
7X-RAY DIFFRACTION6E1 - 110
8X-RAY DIFFRACTION7E115 - 241

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