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- PDB-3dhj: Beta 2 microglobulin mutant W60C -

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Basic information

Entry
Database: PDB / ID: 3dhj
TitleBeta 2 microglobulin mutant W60C
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / beta-2-microglobulin / tryptophan / glycine / amyloidosis / DRA / beta fibrils / Disease mutation / Glycation / Glycoprotein / Immune response / Immunoglobulin domain / MHC I / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib ...regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / 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 epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / focal adhesion / lysosomal membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
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
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRicagno, S. / Colombo, M. / de Rosa, M. / Bolognesi, M. / Giorgetti, S. / Bellotti, V.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2008
Title: DE loop mutations affect beta2-microglobulin stability and amyloid aggregation
Authors: Ricagno, S. / Colombo, M. / de Rosa, M. / Sangiovanni, E. / Giorgetti, S. / Raimondi, S. / Bellotti, V. / Bolognesi, M.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 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 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 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


Theoretical massNumber of molelcules
Total (without water)11,7961
Polymers11,7961
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.353, 28.873, 64.798
Angle α, β, γ (deg.)90.00, 132.53, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11796.290 Da / Num. of mol.: 1 / Mutation: W60C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NM_004048 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M Na acetate, PEG 4000, Ammonium acetate, glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 1, 2008 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 7339 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 16.5 Å2 / Rsym value: 0.033 / Net I/σ(I): 37.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.033 / Mean I/σ(I) obs: 51.5 / Num. unique all: 1052 / Rsym value: 0.033 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2z9t

2z9t


Resolution: 2→19.38 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.428 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.187 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21209 386 5.3 %RANDOM
Rwork0.1729 ---
obs0.17508 6938 99.81 %-
all-7325 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.279 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.02 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms829 0 0 72 901
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022871
X-RAY DIFFRACTIONr_bond_other_d0.0020.02601
X-RAY DIFFRACTIONr_angle_refined_deg1.6151.9441184
X-RAY DIFFRACTIONr_angle_other_deg1.8143.0031463
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8525105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84824.1346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.70215154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.952155
X-RAY DIFFRACTIONr_chiral_restr0.10.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021967
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02181
X-RAY DIFFRACTIONr_mcbond_it0.9711.5511
X-RAY DIFFRACTIONr_mcbond_other0.2671.5200
X-RAY DIFFRACTIONr_mcangle_it1.8352839
X-RAY DIFFRACTIONr_scbond_it2.8133360
X-RAY DIFFRACTIONr_scangle_it4.4394.5342
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 27 -
Rwork0.134 512 -
obs-1052 99.81 %
Refinement TLS params.Method: refined / Origin x: 9.8986 Å / Origin y: -0.7645 Å / Origin z: 15.0827 Å
111213212223313233
T-0.0199 Å20.0031 Å2-0.0039 Å2--0.056 Å20.0076 Å2---0.0325 Å2
L2.5183 °2-0.33 °2-0.9992 °2-0.3975 °20.5187 °2--1.7901 °2
S0.001 Å °0.1545 Å °-0.0112 Å °0.0133 Å °0.0334 Å °0.0016 Å °0.0411 Å °0.0253 Å °-0.0344 Å °

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