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- PDB-7nmf: Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with ... -

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Basic information

Entry
Database: PDB / ID: 7nmf
TitleHuman MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR, monoclinic form
Components
  • (Human T-cell Receptor 4C6, ...) x 2
  • GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
  • 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: 2.98 Å
AuthorsRizkallah, P.J. / Sewell, A.K. / Cole, D.K. / Wall, A.
CitationJournal: To Be Published
Title: Human MHC Class I, A24 Allele presenting QLPRLFPLL, Complex with 4C6 TCR, monoclinic form
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
Revision 1.2Oct 23, 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: Human MHC Class I, beta 2 microglobulin
C: GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU
D: Human T-cell Receptor 4C6, alpha Chain
E: Human T-cell Receptor 4C6, beta Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,3909
Polymers93,9405
Non-polymers4494
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-73 kcal/mol
Surface area38190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.380, 72.250, 114.840
Angle α, β, γ (deg.)90.000, 102.980, 90.000
Int Tables number4
Space group name H-MP1211

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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 GLN-LEU-PRO-ARG-LEU-PHE-PRO-LEU-LEU


Mass: 1097.372 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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

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


Mass: 21636.002 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 T-cell Receptor 4C6, 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, 49 molecules

#6: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.73 Å3/Da / Density % sol: 54.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Sodium Bromide, 0.1 M bis-tris Propane, pH 7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 2.98→60.15 Å / Num. obs: 20168 / % possible obs: 96.6 % / Redundancy: 2.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.088 / Rrim(I) all: 0.158 / Net I/σ(I): 7.8
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
2.98-3.162.90.691951932950.6440.4680.8381.798.1
8.94-60.082.80.03721057470.9960.0250.04421.891.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.5 Å60.08 Å
Translation6.5 Å60.08 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.5.1data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
xia2data reduction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BCK

2bck


Resolution: 2.98→60.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.888 / SU B: 50.907 / SU ML: 0.413 / SU R Cruickshank DPI: 0.3899 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 980 4.9 %RANDOM
Rwork0.1823 ---
obs0.186 19178 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 168.49 Å2 / Biso mean: 61.18 Å2 / Biso min: 21.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-1.56 Å2
2---1.29 Å20 Å2
3---2.09 Å2
Refinement stepCycle: final / Resolution: 2.98→60.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6611 0 26 45 6682
Biso mean--95.37 41.19 -
Num. residues----819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136808
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176119
X-RAY DIFFRACTIONr_angle_refined_deg1.571.6529236
X-RAY DIFFRACTIONr_angle_other_deg1.1851.58414122
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1215814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.30522.198405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.245151126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0771551
X-RAY DIFFRACTIONr_chiral_restr0.0630.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027785
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021653
LS refinement shellResolution: 2.98→3.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.414 70 -
Rwork0.326 1426 -
all-1496 -
obs--98.62 %
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)
12.6712-0.23950.4043.0624-1.28562.965-0.0245-0.02810.1140.0889-0.1014-0.197-0.1676-0.12610.12590.0614-0.0046-0.10190.02770.00330.22131.32220.6835-37.9936
23.1015-0.9270.11423.60643.25986.12250.0699-1.25240.55540.5779-0.1047-0.2148-0.90220.20140.03480.9016-0.47520.00440.7961-0.1090.300311.64898.3769-4.0267
34.2501-0.93641.44834.4768-2.28247.3003-0.0202-0.313-0.12420.4926-0.1044-0.43660.19020.63090.12470.1909-0.0645-0.1570.20650.04840.355422.1683-3.5288-20.205
47.4448-1.00194.54981.4662-0.43355.50630.1475-0.06590.08-0.0034-0.02280.19780.0448-0.3407-0.12460.0281-0.01690.00190.0842-0.05160.2099-24.4847-0.5776-55.6566
54.76480.5598-2.468910.47613.83166.8172-0.05510.3793-0.42540.1165-0.2370.43820.8354-0.40790.2920.2112-0.0044-0.13910.32890.0440.3837-40.5041-5.3419-83.9642
63.09310.24060.62742.97232.79698.26670.00870.369-0.1575-0.2459-0.0485-0.17610.2740.38370.03980.09720.0798-0.00380.16280.04630.253-4.5305-7.0852-67.6494
77.0503-3.81841.23874.5205-0.01042.72430.32380.2383-0.0893-0.364-0.1769-0.04590.05010.1107-0.14690.18210.0186-0.01080.11850.01440.0992-25.4668-1.3405-89.4614
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 - 195
7X-RAY DIFFRACTION6E3 - 112
8X-RAY DIFFRACTION7E113 - 242

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