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- PDB-6i8c: Crystal structure of the murine beta-2-microglobulin. -

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Basic information

Entry
Database: PDB / ID: 6i8c
TitleCrystal structure of the murine beta-2-microglobulin.
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / MHC class I / beta-2-microglobulin / protein aggregation
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / cellular defense response / Neutrophil degranulation / regulation of iron ion transport ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / regulation of membrane depolarization / cellular defense response / Neutrophil degranulation / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / antimicrobial humoral immune response mediated by antimicrobial peptide / negative regulation of neuron projection development / antibacterial humoral response / protein refolding / cellular response to lipopolysaccharide / amyloid fibril formation / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / lysosomal membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / : / 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 ...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
TRIETHYLENE GLYCOL / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsAchour, A. / Sandalova, T. / Ricagno, S. / Sun, R.
CitationJournal: Febs J. / Year: 2020
Title: Biochemical and biophysical comparison of human and mouse beta-2 microglobulin reveals the molecular determinants of low amyloid propensity.
Authors: Achour, A. / Broggini, L. / Han, X. / Sun, R. / Santambrogio, C. / Buratto, J. / Visentin, C. / Barbiroli, A. / De Luca, C.M.G. / Sormanni, P. / Moda, F. / De Simone, A. / Sandalova, T. / ...Authors: Achour, A. / Broggini, L. / Han, X. / Sun, R. / Santambrogio, C. / Buratto, J. / Visentin, C. / Barbiroli, A. / De Luca, C.M.G. / Sormanni, P. / Moda, F. / De Simone, A. / Sandalova, T. / Grandori, R. / Camilloni, C. / Ricagno, S.
History
DepositionNov 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_seq_id / _atom_site.group_PDB ..._atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 2.1Mar 8, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 2.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8552
Polymers11,7041
Non-polymers1501
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint3 kcal/mol
Surface area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.242, 47.603, 64.937
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1 / Mutation: 85D variant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01887
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 40% PEG 6000, 100mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1 Å
DetectorType: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Mar 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→38 Å / Num. obs: 8882 / % possible obs: 98.6 % / Redundancy: 4.4 % / Rsym value: 0.044 / Net I/σ(I): 20.1
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 4.3 % / Num. unique obs: 572 / Rsym value: 0.132 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BII

1bii


Resolution: 1.92→28.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.017 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22186 450 5.1 %RANDOM
Rwork0.18318 ---
obs0.18528 8432 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å2-0 Å2
2---1.42 Å20 Å2
3---1.66 Å2
Refinement stepCycle: 1 / Resolution: 1.92→28.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms812 0 14 87 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.014874
X-RAY DIFFRACTIONr_bond_other_d0.0010.017782
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.6851183
X-RAY DIFFRACTIONr_angle_other_deg0.8031.651850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5295102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65123.48843
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42715160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.97153
X-RAY DIFFRACTIONr_chiral_restr0.0560.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02936
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02156
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_it1.5442.038402
X-RAY DIFFRACTIONr_mcbond_other1.5422.035401
X-RAY DIFFRACTIONr_mcangle_it2.4543.025500
X-RAY DIFFRACTIONr_mcangle_other2.4523.03501
X-RAY DIFFRACTIONr_scbond_it2.0382.365472
X-RAY DIFFRACTIONr_scbond_other2.0382.365472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2563.435682
X-RAY DIFFRACTIONr_long_range_B_refined5.51124.336931
X-RAY DIFFRACTIONr_long_range_B_other5.50824.364932
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.916→1.966 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 35 -
Rwork0.176 589 -
obs--96.45 %

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