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- PDB-1py4: Beta2 microglobulin mutant H31Y displays hints for amyloid formations -

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Basic information

Entry
Database: PDB / ID: 1py4
TitleBeta2 microglobulin mutant H31Y displays hints for amyloid formations
ComponentsBeta-2-microglobulin precursor
KeywordsSIGNALING PROTEIN / amyloid / Dialysis related amyloidosis / C-type immunoglobulin / protein mutant
Function / homology
Function and homology information


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 / 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 ...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 / 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 / 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 / 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: 2.9 Å
AuthorsRosano, C. / Zuccotti, S. / Mangione, P. / Giorgetti, S. / Bellotti, V. / Pettirossi, F. / Corazza, A. / Viglino, P. / Esposito, G. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: beta2-microglobulin H31Y variant 3D structure highlights the protein natural propensity towards intermolecular aggregation
Authors: Rosano, C. / Zuccotti, S. / Mangione, P. / Giorgetti, S. / Bellotti, V. / Pettirossi, F. / Corazza, A. / Viglino, P. / Esposito, G. / Bolognesi, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Preliminary crystallographic characterization of the human beta2 microglobulin in a tetrameric assembly
History
DepositionJul 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin precursor
B: Beta-2-microglobulin precursor
C: Beta-2-microglobulin precursor
D: Beta-2-microglobulin precursor


Theoretical massNumber of molelcules
Total (without water)47,6184
Polymers47,6184
Non-polymers00
Water54030
1
A: Beta-2-microglobulin precursor


Theoretical massNumber of molelcules
Total (without water)11,9041
Polymers11,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-2-microglobulin precursor


Theoretical massNumber of molelcules
Total (without water)11,9041
Polymers11,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-2-microglobulin precursor


Theoretical massNumber of molelcules
Total (without water)11,9041
Polymers11,9041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-2-microglobulin precursor


Theoretical massNumber of molelcules
Total (without water)11,9041
Polymers11,9041
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.195, 150.166, 93.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Beta-2-microglobulin precursor / HDCMA22P


Mass: 11904.383 Da / Num. of mol.: 4 / Fragment: H31Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid details: Site specific mutation / Plasmid: pHN1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4K 31%, glycerol 25%, ammonium acetate 0.2 M, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONELETTRA 5.2R10.927
SYNCHROTRONESRF ID14-420.939
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9271
20.9391
ReflectionResolution: 2.9→30 Å / Num. all: 18871 / Num. obs: 16354 / % possible obs: 99.9 % / Rsym value: 0.069 / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LDS

1lds


Resolution: 2.9→10 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.813 / SU B: 14.417 / SU ML: 0.293 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.935 / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31308 826 5.1 %RANDOM
Rwork0.23961 ---
obs0.24084 15528 100 %-
all-16354 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.002 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å20 Å20 Å2
2--4.75 Å20 Å2
3----3.42 Å2
Refinement stepCycle: LAST / Resolution: 2.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 30 3386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213457
X-RAY DIFFRACTIONr_bond_other_d0.0020.022931
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9374689
X-RAY DIFFRACTIONr_angle_other_deg0.92536861
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3765397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.20.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023805
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02745
X-RAY DIFFRACTIONr_nbd_refined0.3720.21082
X-RAY DIFFRACTIONr_nbd_other0.3630.23826
X-RAY DIFFRACTIONr_nbtor_other0.1060.22142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3180.2115
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.4120.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.530.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it14.29752012
X-RAY DIFFRACTIONr_mcangle_it16.23263287
X-RAY DIFFRACTIONr_scbond_it16.47361445
X-RAY DIFFRACTIONr_scangle_it18.8577.51402
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.969 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.582 45
Rwork0.332 1076

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