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- PDB-3tlr: Crystal Structure of the tetrameric Beta-2 microglobulin DIMC20 mutant -

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Basic information

Entry
Database: PDB / ID: 3tlr
TitleCrystal Structure of the tetrameric Beta-2 microglobulin DIMC20 mutant
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Immunoglobulin-like fold / MHC class I / Light chain
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 ...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: 2.45 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 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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
B: Beta-2-microglobulin
C: Beta-2-microglobulin
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,75216
Polymers47,5824
Non-polymers1,17012
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-21 kcal/mol
Surface area23660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.930, 98.200, 142.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 11895.421 Da / Num. of mol.: 4 / Mutation: S20C
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-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.2 Å3/Da / Density % sol: 44.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.7
Details: Hepes 0.1 M pH 7.7, CdSO4 0.12 M, sodium acetate 2.4 M, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97633 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2010
RadiationMonochromator: Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97633 Å / Relative weight: 1
ReflectionResolution: 2.45→47.5 Å / Num. all: 16174 / Num. obs: 15721 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.39 Å2
Reflection shellResolution: 2.45→2.58 Å / % possible all: 98.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2X4S

2x4s


Resolution: 2.45→19.92 Å / Cor.coef. Fo:Fc: 0.9258 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.748 / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: protgeo_eh99.dat (V1.8) 20110121 STANDARD AMINO ACID DICTIONARY. BONDS AND ANGLES
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 1017 6.5 %RANDOM
Rwork0.2254 ---
obs0.2279 15644 96.53 %-
all-16245 --
Displacement parametersBiso mean: 49.49 Å2
Baniso -1Baniso -2Baniso -3
1--2.6136 Å20 Å20 Å2
2--0.5348 Å20 Å2
3---2.0788 Å2
Refine analyzeLuzzati coordinate error obs: 0.397 Å
Refinement stepCycle: LAST / Resolution: 2.45→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 12 78 3438
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073445HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.014667HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1199SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes96HARMONIC2
X-RAY DIFFRACTIONt_gen_planes0.0131484HARMONIC5
X-RAY DIFFRACTIONt_it3445HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion19.26
X-RAY DIFFRACTIONt_chiral_improper_torsion428SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3345SEMIHARMONIC4
LS refinement shellResolution: 2.45→2.62 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.2823 233 8.26 %
Rwork0.2506 2589 -
all0.2532 2822 -
obs--96.53 %

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