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- PDB-3tm6: Crystal structure of the beta-2 microglobulin DIMC50 disulphide-l... -

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Basic information

Entry
Database: PDB / ID: 3tm6
TitleCrystal structure of the beta-2 microglobulin DIMC50 disulphide-linked homodimer mutant
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / Immunoglobulin-like fold / MHC class I / Light chain
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 / DAP12 interactions / negative regulation of receptor binding / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion ...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 / DAP12 interactions / negative regulation of receptor binding / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / MHC class II protein complex / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi 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 / membrane / identical protein binding / 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 / Immunoglobulins ...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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsColombo, M. / Ricagno, S. / Bolognesi, M.
CitationJournal: Febs J. / Year: 2012
Title: A recurrent D-strand association interface is observed in beta-2 microglobulin oligomers.
Authors: Colombo, M. / de Rosa, M. / Bellotti, V. / Ricagno, S. / Bolognesi, M.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin
E: Beta-2-microglobulin
F: Beta-2-microglobulin
G: Beta-2-microglobulin
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,92819
Polymers94,8278
Non-polymers1,10011
Water2,018112
1
A: Beta-2-microglobulin
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,01710
Polymers47,4144
Non-polymers6036
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-19 kcal/mol
Surface area23610 Å2
MethodPISA
2
E: Beta-2-microglobulin
F: Beta-2-microglobulin
G: Beta-2-microglobulin
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9119
Polymers47,4144
Non-polymers4975
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-21 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.102, 56.272, 96.374
Angle α, β, γ (deg.)90.00, 115.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11853.386 Da / Num. of mol.: 8 / Fragment: Full-length Beta-2 microglobulin / Mutation: E50C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: imidazole-malate 0.2 M, pH 5.5, PEG 600 24%, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2009
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.7→29.39 Å / Num. all: 24109 / Num. obs: 23049 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 65.69 Å2
Reflection shellResolution: 2.7→2.85 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
BUSTER2.11.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z9T

2z9t


Resolution: 2.7→29.39 Å / Cor.coef. Fo:Fc: 0.8738 / Cor.coef. Fo:Fc free: 0.8379 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2625 1160 5.04 %RANDOM
Rwork0.2338 ---
obs0.2353 23013 94.86 %-
all-24326 --
Displacement parametersBiso mean: 43.95 Å2
Baniso -1Baniso -2Baniso -3
1--1.7078 Å20 Å2-0.725 Å2
2--1.1842 Å20 Å2
3---0.5236 Å2
Refine analyzeLuzzati coordinate error obs: 0.419 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6560 0 65 112 6737
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0076802HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19203HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2348SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes0.0095170HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.0116954HARMONIC5
X-RAY DIFFRACTIONt_it6802HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.29
X-RAY DIFFRACTIONt_other_torsion21.25
X-RAY DIFFRACTIONt_chiral_improper_torsion842SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6210SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.2888 136 4.78 %
Rwork0.2531 2710 -
all0.2548 2846 -
obs--94.86 %

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