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- PDB-4rmu: Crystal structure of the D76E Beta-2 Microglobulin mutant -

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Basic information

Entry
Database: PDB / ID: 4rmu
TitleCrystal structure of the D76E 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
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 1.3Nov 20, 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)12,0442
Polymers11,8931
Non-polymers1501
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.401, 28.866, 57.870
Angle α, β, γ (deg.)90.00, 124.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-2-microglobulin


Mass: 11893.383 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 / Mutation: D76E
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 24% 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: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 1, 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: 1.4→47.881 Å / Num. all: 20395 / Num. obs: 20395 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.2
Reflection shellResolution: 1.4→1.48 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 9.4 / % possible all: 82

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YXF

2yxf


Resolution: 1.4→47.881 Å / SU ML: 0.11 / σ(F): 1.34 / Phase error: 18.07 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1921 1999 9.8 %
Rwork0.1632 --
obs0.1661 20394 96.28 %
all-20394 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→47.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 10 147 995
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015889
X-RAY DIFFRACTIONf_angle_d1.6371203
X-RAY DIFFRACTIONf_dihedral_angle_d14.245336
X-RAY DIFFRACTIONf_chiral_restr0.119124
X-RAY DIFFRACTIONf_plane_restr0.008157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.43510.18691120.16281028X-RAY DIFFRACTION75
1.4351-1.47390.21031270.16761176X-RAY DIFFRACTION88
1.4739-1.51720.2081430.16621307X-RAY DIFFRACTION97
1.5172-1.56620.17141430.16081319X-RAY DIFFRACTION99
1.5662-1.62220.17461470.15721358X-RAY DIFFRACTION99
1.6222-1.68710.17931430.16261311X-RAY DIFFRACTION98
1.6871-1.76390.17971470.15611344X-RAY DIFFRACTION99
1.7639-1.85690.17981470.15981357X-RAY DIFFRACTION99
1.8569-1.97330.16711460.1651340X-RAY DIFFRACTION99
1.9733-2.12560.17481440.15381328X-RAY DIFFRACTION98
2.1256-2.33950.1851480.16031362X-RAY DIFFRACTION99
2.3395-2.6780.22621490.17341375X-RAY DIFFRACTION100
2.678-3.37390.20181490.16721378X-RAY DIFFRACTION99
3.3739-47.90870.19951540.16271412X-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)
18.80030.22462.62390.47280.3852.3038-0.24670.28070.2478-0.07440.08290.0112-0.38460.1390.14440.1026-0.01380.00730.03270.01440.1149-17.7714-9.4463-2.3532
26.58423.37660.53724.27550.35161.17240.1431-0.43490.084-0.141-0.1016-0.2926-0.22650.1928-0.06850.0919-0.03580.04640.1562-0.0480.0894.14721.92099.1291
31.8630.08730.55610.97340.58921.4534-0.0337-0.06890.0423-0.04420.02970.0239-0.17060.14530.01540.0672-0.01630.00830.0449-0.00150.0592-10.4444-0.42356.5992
42.5845-0.66330.27071.6434-1.23165.6307-0.046-0.07480.2132-0.0055-0.12460.0465-0.4183-0.14070.1570.09990.0060.00090.0836-0.01460.1681-10.03173.60164.8423
51.70381.20853.0751.84453.68997.5215-0.1050.07980.1016-0.04970.1167-0.0626-0.34970.37650.03090.1146-0.03280.01220.0794-0.01410.0938-6.07193.41674.6497
62.58691.25791.27451.46041.22792.20030.2113-0.5697-0.11330.2515-0.1439-0.03450.1865-0.0659-0.09860.117-0.0269-0.00010.16210.01610.0692-9.4587-3.537115.5125
74.9384-0.46251.68811.9514-0.52312.17710.0452-0.4439-0.70690.00190.0065-0.25410.30080.224-0.07670.16370.0244-0.01160.17230.03880.1418-1.9022-7.136515.4435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 41 )
4X-RAY DIFFRACTION4chain 'A' and (resid 42 through 61 )
5X-RAY DIFFRACTION5chain 'A' and (resid 62 through 69 )
6X-RAY DIFFRACTION6chain 'A' and (resid 70 through 90 )
7X-RAY DIFFRACTION7chain 'A' and (resid 91 through 99 )

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