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- PDB-3ekc: structure of W60V beta-2 microglobulin mutant -

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Basic information

Entry
Database: PDB / ID: 3ekc
Titlestructure of W60V beta-2 microglobulin mutant
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / beta-2-microglobulin / tryptophan / glycine / amyloidosis / DRA / beta fibrils / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


: / : / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...: / : / 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 / cellular response to iron ion / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / 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 ...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 / Immunoglobulin-like fold / Immunoglobulins / 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: 1.8 Å
AuthorsRicagno, S. / Sangiovanni, E. / Bellotti, V. / Bolognesi, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Human beta-2 microglobulin W60V mutant structure: Implications for stability and amyloid aggregation
Authors: Ricagno, S. / Raimondi, S. / Giorgetti, S. / Bellotti, V. / Bolognesi, M.
History
DepositionSep 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)11,7921
Polymers11,7921
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.597, 29.192, 64.538
Angle α, β, γ (deg.)90.00, 132.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11792.277 Da / Num. of mol.: 1 / Mutation: W60V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NM_004048 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O
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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na acetate, PEG 4000, Ammonium acetate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2008 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→47 Å / Num. all: 10083 / Num. obs: 10083 / % possible obs: 99.1 % / Redundancy: 4.2 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.125 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1453 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.4.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2z9t

2z9t


Resolution: 1.8→23.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.437 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 522 5.2 %RANDOM
Rwork0.18437 ---
obs0.18741 9521 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms840 0 0 124 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022862
X-RAY DIFFRACTIONr_bond_other_d0.0030.02594
X-RAY DIFFRACTIONr_angle_refined_deg1.6941.951173
X-RAY DIFFRACTIONr_angle_other_deg2.01531448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4855105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.51523.95343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25115152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.651155
X-RAY DIFFRACTIONr_chiral_restr0.10.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021953
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02179
X-RAY DIFFRACTIONr_mcbond_it1.2141.5511
X-RAY DIFFRACTIONr_mcbond_other0.4521.5200
X-RAY DIFFRACTIONr_mcangle_it1.9062839
X-RAY DIFFRACTIONr_scbond_it2.9023351
X-RAY DIFFRACTIONr_scangle_it4.2224.5331
X-RAY DIFFRACTIONr_rigid_bond_restr1.48431456
X-RAY DIFFRACTIONr_sphericity_free6.6313128
X-RAY DIFFRACTIONr_sphericity_bonded1.9331430
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 33 -
Rwork0.182 697 -
obs--99.32 %

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