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- PDB-7nmc: Crystal structure of beta-2-microglobulin D76E mutant -

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Basic information

Entry
Database: PDB / ID: 7nmc
TitleCrystal structure of beta-2-microglobulin D76E mutant
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / major histocompatibility complex class 1 / beta-2-microglobulin / mutant / D76E
Function / homology
Function and homology information


: / : / 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 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 / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal 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
TRIETHYLENE GLYCOL / 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 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2284
Polymers11,8931
Non-polymers3343
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint2 kcal/mol
Surface area6900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.630, 28.871, 67.508
Angle α, β, γ (deg.)90.000, 102.023, 90.000
Int Tables number5
Space group name H-MI121

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Components

#1: Protein Beta-2-microglobulin


Mass: 11893.383 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.81 % / 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: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.2→46.6 Å / Num. obs: 31346 / % possible obs: 96.3 % / Redundancy: 5.6 % / CC1/2: 0.994 / Rpim(I) all: 0.046 / Net I/σ(I): 12.5
Reflection shellResolution: 1.2→1.22 Å / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1236 / CC1/2: 0.828 / Rpim(I) all: 0.306

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Processing

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

2yxf


Resolution: 1.2→46.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.228 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1794 1499 4.782 %
Rwork0.1582 29846 -
all0.159 --
obs-31345 96.28 %
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: 15.637 Å2
Baniso -1Baniso -2Baniso -3
1-0.415 Å20 Å20.341 Å2
2---0.054 Å20 Å2
3----0.465 Å2
Refinement stepCycle: LAST / Resolution: 1.2→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 22 167 1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013900
X-RAY DIFFRACTIONr_bond_other_d0.0010.017804
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6541214
X-RAY DIFFRACTIONr_angle_other_deg1.4681.5841882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8995104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.00122.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13915156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.962155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2110
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02191
X-RAY DIFFRACTIONr_nbd_refined0.2580.2144
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2150.2737
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2407
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.2437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2103
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.310.213
X-RAY DIFFRACTIONr_nbd_other0.2280.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.229
X-RAY DIFFRACTIONr_mcbond_it1.2731.052407
X-RAY DIFFRACTIONr_mcbond_other1.271.05406
X-RAY DIFFRACTIONr_mcangle_it1.7691.579508
X-RAY DIFFRACTIONr_mcangle_other1.7741.583509
X-RAY DIFFRACTIONr_scbond_it2.8821.649492
X-RAY DIFFRACTIONr_scbond_other2.8811.652493
X-RAY DIFFRACTIONr_scangle_it3.4622.251704
X-RAY DIFFRACTIONr_scangle_other3.4592.254705
X-RAY DIFFRACTIONr_lrange_it4.20816.9441018
X-RAY DIFFRACTIONr_lrange_other3.71515.236967
X-RAY DIFFRACTIONr_rigid_bond_restr2.07931703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.2310.414920.4041775X-RAY DIFFRACTION78.2809
1.231-1.2650.313890.3082023X-RAY DIFFRACTION90.2564
1.265-1.3020.2441020.2262126X-RAY DIFFRACTION98.4099
1.302-1.3420.189940.1712080X-RAY DIFFRACTION98.8631
1.342-1.3850.183990.1462000X-RAY DIFFRACTION98.3599
1.385-1.4340.1791050.1321923X-RAY DIFFRACTION98.8786
1.434-1.4880.1881040.1331864X-RAY DIFFRACTION98.7952
1.488-1.5490.152720.1331815X-RAY DIFFRACTION98.3837
1.549-1.6180.167970.141721X-RAY DIFFRACTION98.4299
1.618-1.6970.153950.1411643X-RAY DIFFRACTION98.8061
1.697-1.7880.178720.1421599X-RAY DIFFRACTION99.228
1.788-1.8960.163770.1391501X-RAY DIFFRACTION98.8103
1.896-2.0270.129560.1281416X-RAY DIFFRACTION98.6595
2.027-2.1890.156680.1351300X-RAY DIFFRACTION97.9943
2.189-2.3980.165690.1341194X-RAY DIFFRACTION97.4537
2.398-2.680.181510.1491080X-RAY DIFFRACTION97.1649
2.68-3.0930.175540.162963X-RAY DIFFRACTION97.3206
3.093-3.7830.165430.146808X-RAY DIFFRACTION96.1582
3.783-5.3330.166340.154646X-RAY DIFFRACTION97.561
5.333-37.8860.254260.273369X-RAY DIFFRACTION96.1071

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