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- PDB-4rmw: Crystal structure of the D76A Beta-2 Microglobulin mutant -

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Basic information

Entry
Database: PDB / ID: 4rmw
TitleCrystal structure of the D76A Beta-2 Microglobulin mutant
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / immunoglobin / beta-sandwitch / amyloidosis / pathologic mutation / genetic disease / MHC class I
Function / homology
Function and homology information


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 / 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 ...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 / 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 / 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 / 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
ACETATE ION / TRIETHYLENE GLYCOL / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
Authorsde Rosa, M. / Bolognesi, M. / Ricagno, S.
CitationJournal: Nat Commun / Year: 2018
Title: Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity.
Authors: Le Marchand, T. / de Rosa, M. / Salvi, N. / Sala, B.M. / Andreas, L.B. / Barbet-Massin, E. / Sormanni, P. / Barbiroli, A. / Porcari, R. / Sousa Mota, C. / de Sanctis, D. / Bolognesi, M. / ...Authors: Le Marchand, T. / de Rosa, M. / Salvi, N. / Sala, B.M. / Andreas, L.B. / Barbet-Massin, E. / Sormanni, P. / Barbiroli, A. / Porcari, R. / Sousa Mota, C. / de Sanctis, D. / Bolognesi, M. / Emsley, L. / Bellotti, V. / Blackledge, M. / Camilloni, C. / Pintacuda, G. / Ricagno, S.
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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)12,0453
Polymers11,8351
Non-polymers2092
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.624, 28.992, 56.293
Angle α, β, γ (deg.)90.00, 127.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-2-microglobulin


Mass: 11835.347 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 / Mutation: D76A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, NM_004048 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.13 Å3/Da / Density % sol: 42.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21% PEG4000, 15% glycerol, 0.2 M ammonium acetate, 0.1 M sodium acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Apr 13, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.4→44.84 Å / Num. all: 19963 / Num. obs: 19921 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 11.7
Reflection shellResolution: 1.4→1.46 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YXF

2yxf


Resolution: 1.4→38.593 Å / SU ML: 0.16 / σ(F): 1.35 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1992 10 %
Rwork0.1796 --
obs0.1829 19920 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→38.593 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms830 0 14 115 959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.021003
X-RAY DIFFRACTIONf_angle_d1.9481374
X-RAY DIFFRACTIONf_dihedral_angle_d15.028390
X-RAY DIFFRACTIONf_chiral_restr0.112142
X-RAY DIFFRACTIONf_plane_restr0.011182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43510.31381420.26221282X-RAY DIFFRACTION100
1.4351-1.47390.28691410.24881266X-RAY DIFFRACTION100
1.4739-1.51730.24411400.21941265X-RAY DIFFRACTION100
1.5173-1.56630.23291400.211258X-RAY DIFFRACTION100
1.5663-1.62220.24581430.1991286X-RAY DIFFRACTION100
1.6222-1.68720.24781410.20191265X-RAY DIFFRACTION100
1.6872-1.7640.2251400.18171268X-RAY DIFFRACTION100
1.764-1.8570.2071410.17831266X-RAY DIFFRACTION100
1.857-1.97330.18631460.17051306X-RAY DIFFRACTION100
1.9733-2.12570.22231380.16851250X-RAY DIFFRACTION100
2.1257-2.33950.19741440.16671290X-RAY DIFFRACTION100
2.3395-2.6780.19561420.17831288X-RAY DIFFRACTION100
2.678-3.37370.20921450.17451294X-RAY DIFFRACTION99
3.3737-38.60790.19541490.16151344X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.67523.28426.26421.65272.8685.2840.03520.1139-0.0929-0.03570.0599-0.03250.02270.0787-0.18230.0772-0.00410.01750.05710.0030.09927.6379-20.559-19.5847
25.8509-2.15030.59327.45250.42820.12350.3631-0.88791.15740.454-0.0145-0.3998-1.23180.5807-0.1880.3458-0.10920.11780.2561-0.12440.311826.9963-4.9824-12.7827
33.7911.15942.80391.72761.50333.84790.0113-0.05760.09430.04960.0139-0.0135-0.1080.0872-0.01480.0786-0.01570.02770.03920.00990.08057.0275-13.6877-15.2306
41.5298-0.00731.1030.7407-1.8554.9266-0.2158-0.37770.47790.3746-0.222-0.063-1.2924-0.47840.27940.34960.0250.00110.2154-0.06350.27197.515-7.2915-11.8626
55.50474.09486.34765.27264.99227.35030.33420.578-0.2313-0.4166-0.1845-0.0160.8349-0.5387-0.11070.24310.02110.00480.2893-0.01890.08593.7261-17.2336-32.7321
64.40012.11893.86635.99384.41987.55180.0862-0.05080.09910.4730.0838-0.3051-0.12650.3524-0.19350.1595-0.02980.01960.10790.00860.158711.9361-9.837-16.0189
72.073-1.0659-2.32880.55771.19852.62820.1446-0.5371-0.04140.79290.2748-0.91010.23771.3868-0.34140.586-0.1433-0.21030.5292-0.02510.362117.269-13.99681.7336
86.30711.72111.89360.73140.10491.11590.3309-0.7683-0.05050.2771-0.34830.01570.3347-0.37370.04820.1003-0.05310.01510.12670.00690.08021.3307-18.6441-11.6458
97.61411.07820.06853.3306-1.53063.79250.2723-0.5299-0.9053-0.0302-0.2018-0.2940.2250.2736-0.05610.1344-0.0041-0.02530.11490.05080.174215.237-20.0694-6.206
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 20 )
3X-RAY DIFFRACTION3chain 'A' and (resid 21 through 41 )
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 56 )
5X-RAY DIFFRACTION5chain 'A' and (resid 57 through 61 )
6X-RAY DIFFRACTION6chain 'A' and (resid 62 through 70 )
7X-RAY DIFFRACTION7chain 'A' and (resid 71 through 77 )
8X-RAY DIFFRACTION8chain 'A' and (resid 78 through 90 )
9X-RAY DIFFRACTION9chain 'A' and (resid 91 through 99 )

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