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- PDB-5cfh: human beta-2 microglobulin double mutant W60G-Y63W -

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Basic information

Entry
Database: PDB / ID: 5cfh
Titlehuman beta-2 microglobulin double mutant W60G-Y63W
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / Aggregation propensity / Amyloid / beta-sandwitch / fold stability
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 / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) 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 / DAP12 interactions / negative regulation of receptor binding / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / 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 / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / 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 / Immunoglobulins ...Beta-2-Microglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsSala, B.M. / De Rosa, M. / Bolognesi, M. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of University and ResearchProject FIRB RBFR109EOS Italy
CitationJournal: Sci Rep / Year: 2016
Title: Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.
Authors: Camilloni, C. / Sala, B.M. / Sormanni, P. / Porcari, R. / Corazza, A. / De Rosa, M. / Zanini, S. / Barbiroli, A. / Esposito, G. / Bolognesi, M. / Bellotti, V. / Vendruscolo, M. / Ricagno, S.
History
DepositionJul 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,7731
Polymers11,7731
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.346, 29.090, 44.410
Angle α, β, γ (deg.)90.00, 113.01, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11773.233 Da / Num. of mol.: 1 / Mutation: W60G, Y63W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET29B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 10000, HEPES

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.49→25.11 Å / Num. obs: 17435 / % possible obs: 95.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.6
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.5 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z9T

2z9t


Resolution: 1.49→25.11 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.929 / SU B: 3.023 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22961 886 5.1 %RANDOM
Rwork0.16892 ---
obs0.17198 16545 95.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.569 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20.57 Å2
2--0.25 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.49→25.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms820 0 0 141 961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.019899
X-RAY DIFFRACTIONr_bond_other_d0.0010.02833
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9441231
X-RAY DIFFRACTIONr_angle_other_deg2.2963.0041937
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9535115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.65224.34846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04915162
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.274155
X-RAY DIFFRACTIONr_chiral_restr0.1060.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211027
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02214
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6992.84419
X-RAY DIFFRACTIONr_mcbond_other4.6972.822418
X-RAY DIFFRACTIONr_mcangle_it5.3484.747528
X-RAY DIFFRACTIONr_mcangle_other5.3444.772529
X-RAY DIFFRACTIONr_scbond_it5.9213.39480
X-RAY DIFFRACTIONr_scbond_other5.7653.359478
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0925.444696
X-RAY DIFFRACTIONr_long_range_B_refined7.3436.9881116
X-RAY DIFFRACTIONr_long_range_B_other7.3646.7171032
X-RAY DIFFRACTIONr_rigid_bond_restr3.57531731
X-RAY DIFFRACTIONr_sphericity_free18.026544
X-RAY DIFFRACTIONr_sphericity_bonded15.56151796
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 69 -
Rwork0.214 1238 -
obs--96.39 %

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