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- PDB-5cka: Human beta-2 microglobulin double mutant W60G-N83V -

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Basic information

Entry
Database: PDB / ID: 5cka
TitleHuman beta-2 microglobulin double mutant W60G-N83V
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Aggregation propensity / Amyloid / beta-sandwitch / fold stability
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 / negative regulation of receptor binding / DAP12 interactions / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma 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 ...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 / DI(HYDROXYETHYL)ETHER / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSala, B.M. / De Rosa, M. / Bolognesi, M. / Ricagno, S.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of University and ResearchFIRB RBFR109EOS Italy
CitationJournal: Sci Rep / Year: 2016
Title: Rational design of mutations that change the aggregation rate of a protein while maintaining its native structure and stability.
Authors: Camilloni, C. / Sala, B.M. / Sormanni, P. / Porcari, R. / Corazza, A. / De Rosa, M. / Zanini, S. / Barbiroli, A. / Esposito, G. / Bolognesi, M. / Bellotti, V. / Vendruscolo, M. / Ricagno, S.
History
DepositionJul 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)12,1446
Polymers11,7351
Non-polymers4085
Water1,27971
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint2 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.980, 28.910, 57.320
Angle α, β, γ (deg.)90.00, 128.57, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-265-

HOH

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Components

#1: Protein Beta-2-microglobulin


Mass: 11735.227 Da / Num. of mol.: 1 / Fragment: resideus 21-119 / Mutation: W60G, N83V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET29B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 M MES, 21% w/v PEG 4000, 15% glycerol, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.7→25.75 Å / Num. obs: 10677 / % possible obs: 96.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2z9t

2z9t


Resolution: 1.7→25.75 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 1068 10.01 %
Rwork0.1763 --
obs0.1813 10671 96.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms819 0 27 71 917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01951
X-RAY DIFFRACTIONf_angle_d1.381291
X-RAY DIFFRACTIONf_dihedral_angle_d15.284363
X-RAY DIFFRACTIONf_chiral_restr0.068134
X-RAY DIFFRACTIONf_plane_restr0.006171
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.27031270.19881188X-RAY DIFFRACTION97
1.7774-1.8710.24061310.19311198X-RAY DIFFRACTION97
1.871-1.98820.25241310.17581166X-RAY DIFFRACTION95
1.9882-2.14170.23981310.17531219X-RAY DIFFRACTION97
2.1417-2.35710.20461310.17551185X-RAY DIFFRACTION96
2.3571-2.69780.26771360.19291186X-RAY DIFFRACTION95
2.6978-3.39770.20531390.17381228X-RAY DIFFRACTION97
3.3977-25.75310.21381420.16571233X-RAY DIFFRACTION96
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)
19.702-2.72147.11313.2561-1.86675.20070.1649-0.1754-0.03740.07690.09010.2120.1349-0.3669-0.22880.13020.01280.01190.0824-0.01260.113742.6656-6.397571.4372
26.7824-7.04154.67178.5685-3.13595.98080.2839-0.2746-0.6294-0.09440.0560.546-0.0871-0.2199-0.34570.1269-0.0205-0.00210.11910.0110.161224.8379-1.036959.6418
36.062-4.8444-0.88644.89910.28132.89830.65231.46120.891-0.5467-0.29880.2325-0.5898-0.7663-0.61610.24140.06430.06440.34910.05290.271214.339710.9656.8858
43.39-4.74463.23936.5663-4.51313.06450.17510.0589-0.2303-0.0915-0.09490.19490.0873-0.1133-0.12090.15110.02150.02210.17350.0070.088228.91672.123361.7016
56.0082-0.82365.34822.4384-1.75638.8432-0.17250.24090.3064-0.00130.0235-0.1151-0.28850.19520.23860.12260.00190.01420.0718-0.0180.147938.71472.496261.1196
67.1301-0.64530.02065.43655.445.5269-0.15470.92891.4306-0.66240.2046-0.6632-1.45860.039-0.17180.4898-0.1076-0.07070.32680.11350.472233.04089.53549.642
76.4769-0.77591.42673.11-0.29046.6287-0.0728-0.58360.0961-0.5190.01110.4255-0.02690.0429-0.0170.1837-0.0424-0.04720.0943-0.03260.148732.96474.860572.2266
86.204-4.06875.62923.6252-4.24985.4437-0.21570.05130.40420.0473-0.1614-0.0542-0.32550.13520.15450.20230.02410.00620.1237-0.01170.125129.58966.865962.5822
99.4139-3.64230.59137.62793.28362.03060.25370.8484-0.614-0.9044-0.24030.62850.1737-0.2887-0.01020.4188-0.0734-0.12190.30810.01220.251722.27844.120144.6278
103.2973-4.40742.58925.8761-3.5052.15850.04010.54440.0158-0.17-0.1877-0.0572-0.11420.30980.08430.1672-0.00190.01180.1656-0.00530.093934.16980.708753.4613
116.1993-0.456-0.93396.0478-1.96342.38940.17490.532-0.2362-0.3185-0.0563-0.52260.7040.3545-0.02290.16620.04870.03090.1514-0.00810.134543.1789-5.618459.2991
128.4019-0.66961.55225.92090.47432.2974-0.0950.1149-0.694-0.21880.11391.41290.4147-0.3159-0.10210.2499-0.073-0.05720.27010.01170.411925.4258-3.841751.9858
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 12 )
3X-RAY DIFFRACTION3chain 'A' and (resid 13 through 21 )
4X-RAY DIFFRACTION4chain 'A' and (resid 22 through 30 )
5X-RAY DIFFRACTION5chain 'A' and (resid 31 through 41 )
6X-RAY DIFFRACTION6chain 'A' and (resid 42 through 50 )
7X-RAY DIFFRACTION7chain 'A' and (resid 51 through 61 )
8X-RAY DIFFRACTION8chain 'A' and (resid 62 through 69 )
9X-RAY DIFFRACTION9chain 'A' and (resid 70 through 77 )
10X-RAY DIFFRACTION10chain 'A' and (resid 78 through 83 )
11X-RAY DIFFRACTION11chain 'A' and (resid 84 through 90 )
12X-RAY DIFFRACTION12chain 'A' and (resid 91 through 99 )

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