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- PDB-4ra3: Crystal structure of dimeric S33C beta-2 microglobulin mutant in ... -

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Basic information

Entry
Database: PDB / ID: 4ra3
TitleCrystal structure of dimeric S33C beta-2 microglobulin mutant in complex with Thioflavin (ThT) at 2.8 Angstrom resolution
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / amyloidosis / protein aggregation / thioflavin / covalent dimer / oligomerization / beta sandwich / inclusion bodies
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
Chem-TFX / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHalabelian, L. / Bolognesi, M. / Ricagno, S.
CitationJournal: Sci Rep / Year: 2015
Title: A covalent homodimer probing early oligomers along amyloid aggregation.
Authors: Halabelian, L. / Relini, A. / Barbiroli, A. / Penco, A. / Bolognesi, M. / Ricagno, S.
History
DepositionSep 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)48,9999
Polymers47,5824
Non-polymers1,4175
Water00
1
A: Beta-2-microglobulin
C: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6415
Polymers23,7912
Non-polymers8503
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-7 kcal/mol
Surface area12300 Å2
MethodPISA
2
B: Beta-2-microglobulin
D: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3584
Polymers23,7912
Non-polymers5672
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-9 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.038, 80.038, 177.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPAA1 - 962 - 97
21ASPASPBB1 - 962 - 97
12ASPASPAA1 - 982 - 99
22ASPASPCC1 - 982 - 99
13ASPASPAA1 - 982 - 99
23ASPASPDD1 - 982 - 99
14ASPASPBB1 - 962 - 97
24ASPASPCC1 - 962 - 97
15ASPASPBB1 - 962 - 97
25ASPASPDD1 - 962 - 97
16METMETCC1 - 992 - 100
26METMETDD1 - 992 - 100

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Beta-2-microglobulin


Mass: 11895.422 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119 / Mutation: S33C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P, NM_004048 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#2: Chemical
ChemComp-TFX / 2-[4-(dimethylamino)phenyl]-3,6-dimethyl-1,3-benzothiazol-3-ium / Thioflavin T


Mass: 283.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C17H19N2S

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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: 3.45 Å3/Da / Density % sol: 64.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% v/v PEG4000, 0.1 M sodium chloride, 5 mM thioflavin, 0.1 M HEPES sodium, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97088 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 14, 2014
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97088 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.463
11-h,-k,l20.537
ReflectionResolution: 2.8→177.7 Å / Num. all: 16940 / Num. obs: 16940 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 21.4
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 10 % / Rmerge(I) obs: 1.139 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
BALBESphasing
REFMAC5.8.0069refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3S6C

3s6c


Resolution: 2.8→69.31 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.558 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20649 862 5.1 %RANDOM
Rwork0.17075 ---
obs0.17252 16036 99.91 %-
all-16940 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 113.054 Å2
Baniso -1Baniso -2Baniso -3
1-26.34 Å20 Å20 Å2
2--26.34 Å20 Å2
3----52.68 Å2
Refinement stepCycle: LAST / Resolution: 2.8→69.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3307 0 100 0 3407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193514
X-RAY DIFFRACTIONr_bond_other_d0.0010.023203
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9254773
X-RAY DIFFRACTIONr_angle_other_deg1.54837376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9265391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.45423.966179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.40815591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.3871520
X-RAY DIFFRACTIONr_chiral_restr0.0840.2479
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214410
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02858
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.82311.0821576
X-RAY DIFFRACTIONr_mcbond_other6.81911.0791575
X-RAY DIFFRACTIONr_mcangle_it9.8116.6061963
X-RAY DIFFRACTIONr_mcangle_other9.73416.2081964
X-RAY DIFFRACTIONr_scbond_it7.3311.4761938
X-RAY DIFFRACTIONr_scbond_other7.20411.2091939
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.51916.6062811
X-RAY DIFFRACTIONr_long_range_B_refined13.1352955
X-RAY DIFFRACTIONr_long_range_B_other13.1332956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A50210.15
12B50210.15
21A52830.14
22C52830.14
31A51210.16
32D51210.16
41B49940.16
42C49940.16
51B49360.17
52D49360.17
61C53170.15
62D53170.15
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.798 68 -
Rwork0.525 1171 -
obs--99.84 %

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