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- PDB-6y27: Crystal structure of HLA-B2709 complexed with the nona-peptide mA -

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Basic information

Entry
Database: PDB / ID: 6y27
TitleCrystal structure of HLA-B2709 complexed with the nona-peptide mA
Components
  • Beta-2-microglobulin
  • Lymphocyte antigen HLA-B27
  • mA
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: 1.38 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 1.2Nov 20, 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: Lymphocyte antigen HLA-B27
B: Beta-2-microglobulin
C: mA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1117
Polymers44,8003
Non-polymers3124
Water11,313628
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-27 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.060, 82.720, 110.310
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

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Protein , 2 types, 2 molecules AB

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide mA


Mass: 969.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)

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Non-polymers , 3 types, 632 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.6 Å3/Da / Density % sol: 52.69 %
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: Jul 17, 2004
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. obs: 95918 / % possible obs: 99.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 17.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.9
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 12759 / CC1/2: 0.303 / Rrim(I) all: 2.02 / % possible all: 97

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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: 1.38→27.77 Å / SU ML: 0.2357 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9128
RfactorNum. reflection% reflection
Rfree0.1941 4772 5 %
Rwork0.1581 --
obs0.1599 95529 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.02 Å2
Refinement stepCycle: LAST / Resolution: 1.38→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 19 628 3806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01263569
X-RAY DIFFRACTIONf_angle_d1.23234871
X-RAY DIFFRACTIONf_chiral_restr0.1061502
X-RAY DIFFRACTIONf_plane_restr0.0086645
X-RAY DIFFRACTIONf_dihedral_angle_d17.2671409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.41.00181220.92782391X-RAY DIFFRACTION79.45
1.4-1.410.54541550.50062948X-RAY DIFFRACTION97.39
1.41-1.430.41631580.37883003X-RAY DIFFRACTION98.94
1.43-1.450.36121560.31662962X-RAY DIFFRACTION99.39
1.45-1.470.29091600.27863048X-RAY DIFFRACTION99.6
1.47-1.490.30461580.2553004X-RAY DIFFRACTION99.81
1.49-1.510.29211580.23013005X-RAY DIFFRACTION99.06
1.51-1.530.25241600.2033022X-RAY DIFFRACTION99.66
1.53-1.550.25391570.19752994X-RAY DIFFRACTION99.09
1.55-1.580.27631590.17943023X-RAY DIFFRACTION99.66
1.58-1.610.22271580.1713008X-RAY DIFFRACTION99.47
1.61-1.640.19441600.16143028X-RAY DIFFRACTION99.81
1.64-1.670.20841600.16323035X-RAY DIFFRACTION99.72
1.67-1.70.20581600.1633053X-RAY DIFFRACTION99.81
1.7-1.740.20541590.15983008X-RAY DIFFRACTION99.75
1.74-1.780.19951600.14463047X-RAY DIFFRACTION99.81
1.78-1.820.18451610.14523064X-RAY DIFFRACTION99.85
1.82-1.870.18821600.1373026X-RAY DIFFRACTION99.91
1.87-1.930.18251610.13523066X-RAY DIFFRACTION99.91
1.93-1.990.17131590.13083033X-RAY DIFFRACTION99.78
1.99-2.060.16851620.12753065X-RAY DIFFRACTION99.78
2.06-2.140.16291610.1313053X-RAY DIFFRACTION99.88
2.14-2.240.16161600.14153054X-RAY DIFFRACTION99.75
2.24-2.360.21741620.14293078X-RAY DIFFRACTION99.94
2.36-2.510.20041630.15183097X-RAY DIFFRACTION99.85
2.51-2.70.19971630.16553088X-RAY DIFFRACTION99.88
2.7-2.970.18991620.15683083X-RAY DIFFRACTION99.75
2.97-3.40.1871640.15023111X-RAY DIFFRACTION99.6
3.4-4.280.14761650.13163144X-RAY DIFFRACTION99.43
4.28-27.770.14351690.13983216X-RAY DIFFRACTION97.16

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