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- PDB-4rmv: Crystal structure of the D76H Beta-2 Microglobulin mutant -

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Basic information

Entry
Database: PDB / ID: 4rmv
TitleCrystal structure of the D76H 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


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 / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...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 / cellular response to iron ion / 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 / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / 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 / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / 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 / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / 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 / 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 / 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
ACETATE ION / TRIETHYLENE GLYCOL / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.463 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 / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1123
Polymers11,9021
Non-polymers2092
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.540, 28.871, 53.280
Angle α, β, γ (deg.)90.00, 125.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-102-

PGE

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Components

#1: Protein Beta-2-microglobulin


Mass: 11902.416 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 / Mutation: D76H
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 76 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% PEG4000, 15% glycerol, 0.2 M ammonium acetate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 15, 2014 / Details: bent cylindrical mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.46→21.612 Å / Num. all: 16702 / Num. obs: 16365 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.3
Reflection shellResolution: 1.46→1.54 Å / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7

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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: 1.463→21.612 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 26.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2286 1633 10 %
Rwork0.1856 --
obs0.1899 16323 97.17 %
all-16323 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.463→21.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 14 76 929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007973
X-RAY DIFFRACTIONf_angle_d1.1661327
X-RAY DIFFRACTIONf_dihedral_angle_d14.905384
X-RAY DIFFRACTIONf_chiral_restr0.081136
X-RAY DIFFRACTIONf_plane_restr0.005172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.463-1.5060.37511370.31211220X-RAY DIFFRACTION98
1.506-1.55460.27881320.27171213X-RAY DIFFRACTION97
1.5546-1.61020.27851360.23881219X-RAY DIFFRACTION97
1.6102-1.67460.27721300.23671162X-RAY DIFFRACTION94
1.6746-1.75080.27531380.20331240X-RAY DIFFRACTION99
1.7508-1.84310.24131360.20391228X-RAY DIFFRACTION98
1.8431-1.95850.24141310.19271178X-RAY DIFFRACTION94
1.9585-2.10960.20951390.17431242X-RAY DIFFRACTION98
2.1096-2.32160.2231390.1781255X-RAY DIFFRACTION99
2.3216-2.65710.22791330.17891192X-RAY DIFFRACTION95
2.6571-3.34560.2121390.17811260X-RAY DIFFRACTION98
3.3456-21.61470.20581430.15921281X-RAY DIFFRACTION97
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)
13.5527-3.5064.81422.913-3.38846.47020.00310.026-0.15320.04570.15070.1523-0.0021-0.0025-0.26060.1096-0.00390.02070.0838-0.00380.126872.2039-19.526819.7942
25.1474-2.3452.70347.0565-3.00481.94130.39860.95660.64810.40290.28281.001-0.691-1.0447-0.39790.26140.11620.11530.350.14340.358752.0398-4.54710.314
35.6802-5.21125.55474.0712-4.86894.4820.0342-0.1386-0.2618-0.01380.1260.18970.0828-0.2805-0.22240.12510.01460.00560.13420.00410.137267.4848-13.501516.132
44.0865-0.5182.29612.31910.85124.3806-0.29610.5220.3944-0.2398-0.011-0.0764-0.99340.11590.24020.2099-0.00150.00190.17860.03060.186174.3296-9.43939.5323
57.491-2.0562.38257.3141-4.88624.3344-0.0826-0.23050.7556-0.42350.18940.506-0.8882-0.18370.02460.28220.0028-0.00160.1244-0.01490.262670.1179-7.058422.3563
64.1239-3.67332.18294.4993-4.32945.7694-0.0849-1.63-1.13521.73-0.4407-1.0221.77340.99550.39020.650.0295-0.090.48140.16670.37275.3728-17.319832.1335
77.9092-4.73261.96456.88080.3551.92470.20030.27660.1765-0.2946-0.30940.2481-0.27660.1077-0.15360.1209-0.0160.00640.08740.01210.139367.5295-8.603916.4108
86.40411.45980.70434.47173.98133.4607-0.11430.7703-0.15-0.8292-0.17580.4658-0.5627-0.13420.36310.34520.0446-0.07780.29560.01090.203361.133-12.0864-1.2942
93.175-2.02492.79852.0992-1.00113.94740.15250.51520.216-0.3118-0.2225-0.20420.25430.20220.15050.1290.02810.03110.1490.00230.110277.3176-17.891110.8484
104.9593-1.6454.98032.04650.27158.45990.0091-0.1331-1.268-0.057-0.09460.92480.3099-0.51190.01590.1874-0.0024-0.05790.1688-0.06910.42864.1948-19.62346.9172
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 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 30 )
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 50 )
5X-RAY DIFFRACTION5chain 'A' and (resid 51 through 56 )
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 61 )
7X-RAY DIFFRACTION7chain 'A' and (resid 62 through 69 )
8X-RAY DIFFRACTION8chain 'A' and (resid 70 through 77 )
9X-RAY DIFFRACTION9chain 'A' and (resid 78 through 90 )
10X-RAY DIFFRACTION10chain 'A' and (resid 91 through 99 )

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