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- PDB-7nmt: Crystal structure of beta-2-microglobulin D76G mutant -

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Basic information

Entry
Database: PDB / ID: 7nmt
TitleCrystal structure of beta-2-microglobulin D76G mutant
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / major histocompatibility complex class 1 / beta-2-microglobulin / mutant / D76G
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsGuthertz, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustRGIMCB-109984 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: The effect of mutation on an aggregation-prone protein: An in vivo, in vitro, and in silico analysis.
Authors: Guthertz, N. / van der Kant, R. / Martinez, R.M. / Xu, Y. / Trinh, C. / Iorga, B.I. / Rousseau, F. / Schymkowitz, J. / Brockwell, D.J. / Radford, S.E.
History
DepositionFeb 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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
AAA: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,8211
Polymers11,8211
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.542, 28.683, 62.473
Angle α, β, γ (deg.)90.000, 98.466, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Beta-2-microglobulin


Mass: 11821.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.08 Å3/Da / Density % sol: 40.92 % / Description: One molecule per asymmetric unit
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 100 nL mother liquor / 200 nL protein 15% Glycerol, 0.1 M NaAcetate pH 4.5-5.5, 28-32%PEG 4000, 0.2 M NH4Acetate
PH range: 4.5 - 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.2→44.43 Å / Num. obs: 30235 / % possible obs: 98.4 % / Redundancy: 2.6 % / CC1/2: 0.997 / Rpim(I) all: 0.037 / Net I/σ(I): 10.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1458 / CC1/2: 0.911 / Rpim(I) all: 0.219 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimlessdata reduction
Cootmodel building
PHASERphasing
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2YXF

2yxf


Resolution: 1.2→44.43 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.703 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.04
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.174 1517 5.018 %
Rwork0.1388 28717 -
all0.141 --
obs-30234 98.188 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.025 Å20 Å2-0.039 Å2
2---1.222 Å20 Å2
3---1.158 Å2
Refinement stepCycle: LAST / Resolution: 1.2→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 0 162 995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.013880
X-RAY DIFFRACTIONr_bond_other_d0.0030.017782
X-RAY DIFFRACTIONr_angle_refined_deg2.1391.6531199
X-RAY DIFFRACTIONr_angle_other_deg1.5761.581829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9525107
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26122.650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.65815154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.528155
X-RAY DIFFRACTIONr_chiral_restr0.1050.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02990
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02193
X-RAY DIFFRACTIONr_nbd_refined0.1910.2149
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.2740
X-RAY DIFFRACTIONr_nbtor_refined0.1730.2416
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2479
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3030.219
X-RAY DIFFRACTIONr_nbd_other0.2410.262
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2630.231
X-RAY DIFFRACTIONr_mcbond_it1.9491.14410
X-RAY DIFFRACTIONr_mcbond_other1.9511.14409
X-RAY DIFFRACTIONr_mcangle_it2.6191.72514
X-RAY DIFFRACTIONr_mcangle_other2.6171.719515
X-RAY DIFFRACTIONr_scbond_it3.8251.696470
X-RAY DIFFRACTIONr_scbond_other3.8241.699470
X-RAY DIFFRACTIONr_scangle_it4.5682.322682
X-RAY DIFFRACTIONr_scangle_other4.5682.325682
X-RAY DIFFRACTIONr_lrange_it4.87817.5761021
X-RAY DIFFRACTIONr_lrange_other4.25615.944965
X-RAY DIFFRACTIONr_rigid_bond_restr9.58631662
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.2-1.2310.3031170.24320640.24622560.9360.95296.67550.204
1.231-1.2650.219970.20520740.20622300.9640.95897.35430.171
1.265-1.3010.2021040.18619630.18721300.9560.95697.04230.159
1.301-1.3420.1841000.1619150.16120610.9620.95897.76810.139
1.342-1.3850.19930.14719090.14920310.9410.96398.57210.127
1.385-1.4340.1651030.13418380.13619600.9610.9799.03060.119
1.434-1.4880.184970.13117540.13318710.9640.97298.93110.118
1.488-1.5490.184830.13317020.13518000.9540.96799.16670.123
1.549-1.6180.1841120.12416200.12717460.960.97599.19820.115
1.618-1.6960.155790.11815760.11916800.9690.97898.51190.11
1.696-1.7880.172990.11714660.12115890.9670.97798.48960.114
1.788-1.8960.145750.10914080.11115090.9810.9898.2770.109
1.896-2.0270.119720.10713060.10713980.9840.98598.56940.113
2.027-2.1890.166650.11612280.11913260.9640.97997.51130.123
2.189-2.3970.156430.12211690.12312320.9680.97598.37660.133
2.397-2.6790.173510.13110260.13310920.9690.97598.62640.146
2.679-3.0920.24360.1419390.1449880.9260.96498.68420.162
3.092-3.7820.148390.1357870.1368440.9730.97597.86730.164
3.782-5.330.136230.1456270.1446600.9760.97398.48480.19
5.33-44.4340.227290.2443460.2433890.9570.94296.4010.315

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