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- PDB-3loz: Crystal structure of Beta 2 Microglobulin amyloidogenic segment LSFSKD -

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Basic information

Entry
Database: PDB / ID: 3loz
TitleCrystal structure of Beta 2 Microglobulin amyloidogenic segment LSFSKD
ComponentsBeta-2-microglobulin segment LSFSKD
KeywordsPROTEIN FIBRIL / steric zipper / beta spine / beta 2 microglobulin
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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent ...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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / 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 / 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 / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLiu, C. / Sawaya, M. / Eisenberg, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Beta2-microglobulin forms three-dimensional domain-swapped amyloid fibrils with disulfide linkages.
Authors: Liu, C. / Sawaya, M.R. / Eisenberg, D.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-2-microglobulin segment LSFSKD
B: Beta-2-microglobulin segment LSFSKD
C: Beta-2-microglobulin segment LSFSKD
D: Beta-2-microglobulin segment LSFSKD


Theoretical massNumber of molelcules
Total (without water)2,7874
Polymers2,7874
Non-polymers00
Water30617
1
A: Beta-2-microglobulin segment LSFSKD
B: Beta-2-microglobulin segment LSFSKD

C: Beta-2-microglobulin segment LSFSKD
D: Beta-2-microglobulin segment LSFSKD

A: Beta-2-microglobulin segment LSFSKD
B: Beta-2-microglobulin segment LSFSKD
C: Beta-2-microglobulin segment LSFSKD
D: Beta-2-microglobulin segment LSFSKD


Theoretical massNumber of molelcules
Total (without water)5,5748
Polymers5,5748
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_655x+1,y,z1
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)9.425, 21.482, 45.731
Angle α, β, γ (deg.)90.000, 90.02, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Beta-2-microglobulin segment LSFSKD


Mass: 696.770 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: UniProt: P61769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 1.66 Å3/Da / Density % sol: 25.95 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 1656 / % possible obs: 93.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.118 / Χ2: 2.393 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.863.70.5011502.094182
1.86-1.943.60.3291332.411182.1
1.94-2.033.70.2471472.325188.6
2.03-2.133.70.2031582.719192.9
2.13-2.273.90.2151742.135197.2
2.27-2.444.10.2051872.493198.9
2.44-2.694.30.1891632.3131100
2.69-3.0840.1211842.928198.9
3.08-3.883.60.0761722.449198.9
3.88-803.50.0361881.98196.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→22.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.971 / Occupancy max: 1 / Occupancy min: 0 / SU B: 4.689 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 175 10.5 %RANDOM
Rwork0.216 ---
obs0.219 1499 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 34.22 Å2 / Biso mean: 16.931 Å2 / Biso min: 8.43 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20.05 Å2
2--4.13 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms196 0 0 17 213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022204
X-RAY DIFFRACTIONr_bond_other_d0.0010.02146
X-RAY DIFFRACTIONr_angle_refined_deg0.9792.045270
X-RAY DIFFRACTIONr_angle_other_deg0.6593362
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.188524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.297258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9921542
X-RAY DIFFRACTIONr_chiral_restr0.0660.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02214
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0242
X-RAY DIFFRACTIONr_mcbond_it1.0021.5126
X-RAY DIFFRACTIONr_mcbond_other0.2721.546
X-RAY DIFFRACTIONr_mcangle_it2.0442200
X-RAY DIFFRACTIONr_scbond_it2.609378
X-RAY DIFFRACTIONr_scangle_it3.4044.568
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 10 -
Rwork0.257 97 -
all-107 -
obs--84.25 %

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