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- PDB-7nmg: Human MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR -

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Basic information

Entry
Database: PDB / ID: 7nmg
TitleHuman MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR
Components
  • (Human 4C6 T-cell Receptor, ...) x 2
  • Diabetes epitope LWMRLLPLL
  • Human MHC Class I, beta 2 microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / MHC Class I / A24 / Diabetes related super antigen / 4C6 TCR
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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / 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 immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / 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 / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / 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 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. ...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
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: 2.48 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Cole, D.K. / Wall, A.
CitationJournal: To Be Published
Title: Human MHC Class I, A24 Allele presenting LWM, Complex with 4C6 TCR
Authors: Rizkallahp, P.J. / Sewell, A.K. / Cole, D.K. / Wall, A.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: Human MHC Class I, beta 2 microglobulin
C: Diabetes epitope LWMRLLPLL
D: Human 4C6 T-cell Receptor, alpha Chain
E: Human 4C6 T-cell Receptor, beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,48512
Polymers93,7725
Non-polymers7137
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-90 kcal/mol
Surface area38040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.320, 72.130, 230.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen


Mass: 31778.117 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: A0A411J078
#2: Protein Human MHC Class I, beta 2 microglobulin / 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 Diabetes epitope LWMRLLPLL


Mass: 1155.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Human 4C6 T-cell Receptor, ... , 2 types, 2 molecules DE

#4: Protein Human 4C6 T-cell Receptor, alpha Chain


Mass: 21409.773 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 4C6 T-cell Receptor, beta Chain


Mass: 27549.529 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 , 4 types, 119 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500, 0.1M PCTP Buffer, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.48→52.93 Å / Num. obs: 33057 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.05 / Rrim(I) all: 0.108 / Net I/σ(I): 11.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.48-2.584.41.311632136920.5130.691.4861.399.9
8.94-52.873.80.02230187970.9990.0120.02535.498.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.86 Å52.87 Å
Translation4.86 Å52.87 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.27data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.48→52.93 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.916 / SU B: 28.683 / SU ML: 0.29 / SU R Cruickshank DPI: 0.6244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.624 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1616 4.9 %RANDOM
Rwork0.1977 ---
obs0.2013 31375 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.24 Å2 / Biso mean: 51.78 Å2 / Biso min: 25.16 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20 Å2
2---0.15 Å20 Å2
3----0.68 Å2
Refinement stepCycle: final / Resolution: 2.48→52.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 42 112 6752
Biso mean--85.99 44.16 -
Num. residues----817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136820
X-RAY DIFFRACTIONr_bond_other_d0.0020.0176134
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.6539249
X-RAY DIFFRACTIONr_angle_other_deg1.1831.58414151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.3965814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54522.153404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.286151128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0251551
X-RAY DIFFRACTIONr_chiral_restr0.0640.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027783
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021659
LS refinement shellResolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 116 -
Rwork0.323 2246 -
all-2362 -
obs--99.87 %
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)
12.2584-0.94220.14032.6613-0.35623.21680.0314-0.1049-0.06560.1146-0.0887-0.02420.0760.16510.05730.2485-0.0180.03130.0447-0.01910.03724.854135.581930.6413
22.03962.79971.25257.33083.81755.0225-0.01130.2381-0.1455-0.6772-0.13380.27420.1146-0.50720.14510.24960.0474-0.06190.1675-0.05830.1324.507126.26783.0099
34.4754-0.89881.05253.4966-1.43035.67570.1290.51720.1363-0.4811-0.1168-0.0635-0.40130.2192-0.01220.3398-0.05370.0930.0842-0.01410.042122.678239.61983.3949
41.38570.2504-0.10421.1674-0.51648.18550.0146-0.1434-0.13520.13120.00240.16090.0577-0.2126-0.0170.2404-0.00440.04630.1022-0.06720.165923.55536.978361.6303
54.47882.44010.93417.18231.96493.87880.0497-0.43890.81160.339-0.0970.3465-0.47470.01590.04730.44870.02380.07510.22240.02090.218336.603841.432491.4394
66.30452.5432.34423.23882.03914.1990.10790.02990.22080.2087-0.0098-0.4284-0.26080.5616-0.09810.3145-0.04080.0310.2214-0.02350.185345.120943.314852.8398
72.80271.9928-1.47284.0636-2.09514.99260.1065-0.0083-0.09440.0838-0.0547-0.2423-0.18330.4005-0.05170.24750.0185-0.05080.17-0.07420.168749.870937.509282.6267
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 DIFFRACTION3B0 - 99
5X-RAY DIFFRACTION4D2 - 113
6X-RAY DIFFRACTION5D114 - 193
7X-RAY DIFFRACTION6E3 - 112
8X-RAY DIFFRACTION7E113 - 242

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