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- PDB-6y2b: Crystal structure of HLA-B2709 complexed with the nona-peptide mQ -

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Basic information

Entry
Database: PDB / ID: 6y2b
TitleCrystal structure of HLA-B2709 complexed with the nona-peptide mQ
Components
  • Beta-2-microglobulin
  • Lymphocyte antigen HLA-B27
  • mQ
KeywordsIMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC MAJOR HISTOCOMPATIBILITY COMPLEX / HLA- B*2709
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...antigen processing and presentation of peptide antigen via MHC class I / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex / 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 / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / 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, alpha chain, C-terminal / MHC_I C-terminus / 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, alpha chain, C-terminal / MHC_I C-terminus / 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
Lymphocyte antigen HLA-B27 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å
AuthorsLoll, B. / Rueckert, C. / Ziegler, B.-U. / Ziegler, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SfB 449 Germany
CitationJournal: to be published
Title: A CENTRAL PEPTIDE RESIDUE CAN CONTROL MHC POLYMORPHISM-DEPENDENT ANTIGEN PRESENTATION
Authors: Loll, B. / Rueckert, C. / Ziegler, B.-U. / Ziegler, A.
History
DepositionFeb 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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

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Assembly

Deposited unit
A: Lymphocyte antigen HLA-B27
B: Beta-2-microglobulin
C: mQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2257
Polymers44,8573
Non-polymers3684
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-18 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.768, 82.214, 109.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Lymphocyte antigen HLA-B27 / MHC class I antigen


Mass: 31951.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2R7Z5J3
#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 / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide mQ


Mass: 1026.233 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 681 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% (w/v) PEG8000, 150 mM NaCl and 100 mM Tris-HCl, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 19, 2004
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. obs: 95619 / % possible obs: 98.2 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.13 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.05 / Net I/σ(I): 25.5
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 4.7 % / Num. unique obs: 14111 / CC1/2: 0.959 / Rrim(I) all: 0.273 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
DNAdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2A83

2a83


Resolution: 1.37→27.88 Å / SU ML: 0.1215 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.9377
RfactorNum. reflection% reflection
Rfree0.1809 2096 2.19 %
Rwork0.1416 --
obs0.1425 95555 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.13 Å2
Refinement stepCycle: LAST / Resolution: 1.37→27.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 24 681 3868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01173629
X-RAY DIFFRACTIONf_angle_d1.26554969
X-RAY DIFFRACTIONf_chiral_restr0.1073503
X-RAY DIFFRACTIONf_plane_restr0.0092671
X-RAY DIFFRACTIONf_dihedral_angle_d17.21951427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.37-1.40.22361180.16025244X-RAY DIFFRACTION83.82
1.4-1.430.19751320.1415915X-RAY DIFFRACTION94.5
1.43-1.470.1711400.12766228X-RAY DIFFRACTION99.27
1.47-1.520.14691410.12046287X-RAY DIFFRACTION100
1.52-1.570.17631360.14186188X-RAY DIFFRACTION98.78
1.57-1.620.17631420.12426286X-RAY DIFFRACTION99.78
1.62-1.690.16911410.12716316X-RAY DIFFRACTION99.98
1.69-1.760.17981420.12946295X-RAY DIFFRACTION100
1.76-1.860.18131420.13576329X-RAY DIFFRACTION100
1.86-1.970.17731420.13236316X-RAY DIFFRACTION99.91
1.97-2.130.17711420.13256336X-RAY DIFFRACTION99.97
2.13-2.340.18551430.14016380X-RAY DIFFRACTION99.98
2.34-2.680.17521440.1526404X-RAY DIFFRACTION100
2.68-3.370.18251450.14966450X-RAY DIFFRACTION99.92
3.37-27.880.18841460.1526485X-RAY DIFFRACTION96.8

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