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- PDB-6y29: Crystal structure of HLA-B2709 complexed with the nona-peptide mE -

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Basic information

Entry
Database: PDB / ID: 6y29
TitleCrystal structure of HLA-B2709 complexed with the nona-peptide mE
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Lymphocyte antigen HLA-B27
  • mE
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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway ...antigen processing and presentation of peptide antigen via MHC class I / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / 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 exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...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: 1.28 Å
AuthorsLoll, B. / Rueckert, C. / Ziegler, B.-U. / Ziegler, A.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SfB 449
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

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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: mE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2267
Polymers44,8583
Non-polymers3684
Water11,836657
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-18 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.876, 83.136, 110.832
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 / 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 mE


Mass: 1027.218 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 / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 657 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.61 Å3/Da / Density % sol: 52.92 %
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: Nov 30, 2003
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.28→30 Å / Num. obs: 119012 / % possible obs: 97.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.072 / Net I/σ(I): 13.3
Reflection shellResolution: 1.28→1.36 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 17486 / CC1/2: 0.631 / Rrim(I) all: 0.883 / % possible all: 89.7

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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: 1.28→24.79 Å / SU ML: 0.1223 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.4973
RfactorNum. reflection% reflection
Rfree0.1694 2100 1.76 %
Rwork0.1406 --
obs0.1411 118991 97.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.86 Å2
Refinement stepCycle: LAST / Resolution: 1.28→24.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3163 0 24 657 3844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01583582
X-RAY DIFFRACTIONf_angle_d1.42934889
X-RAY DIFFRACTIONf_chiral_restr0.1094495
X-RAY DIFFRACTIONf_plane_restr0.0109655
X-RAY DIFFRACTIONf_dihedral_angle_d17.11711404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.310.32371180.27626544X-RAY DIFFRACTION82.88
1.31-1.340.30341320.25367345X-RAY DIFFRACTION92.85
1.34-1.380.26331390.21617778X-RAY DIFFRACTION99.11
1.38-1.420.20991420.17667894X-RAY DIFFRACTION99.84
1.42-1.460.19591410.1567862X-RAY DIFFRACTION99.79
1.46-1.520.18841420.14277901X-RAY DIFFRACTION99.78
1.52-1.580.1621420.12847900X-RAY DIFFRACTION99.89
1.58-1.650.16531430.1167941X-RAY DIFFRACTION99.88
1.65-1.740.17371430.11827935X-RAY DIFFRACTION99.9
1.74-1.840.15481420.12327949X-RAY DIFFRACTION99.93
1.84-1.990.16251430.12137959X-RAY DIFFRACTION99.95
1.99-2.190.13711440.11297991X-RAY DIFFRACTION99.91
2.19-2.50.15661440.12548036X-RAY DIFFRACTION99.82
2.5-3.150.15621460.14118085X-RAY DIFFRACTION99.66
3.15-24.790.16061390.14817771X-RAY DIFFRACTION92.57

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