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- PDB-2f8o: A Native to Amyloidogenic Transition Regulated by a Backbone Trigger -

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Basic information

Entry
Database: PDB / ID: 2f8o
TitleA Native to Amyloidogenic Transition Regulated by a Backbone Trigger
ComponentsBeta-2-microglobulinBeta-2 microglobulin
KeywordsIMMUNE SYSTEM / beta-sandwich / amyloid / class-1 MHC
Function / homology
Function and homology information


positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / early endosome lumen / positive regulation of receptor binding / 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 / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / 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 / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / 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 / endoplasmic reticulum lumen / external side of plasma membrane / 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
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEakin, C.M. / Berman, A.J. / Miranker, A.D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: A native to amyloidogenic transition regulated by a backbone trigger.
Authors: Eakin, C.M. / Berman, A.J. / Miranker, A.D.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: 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 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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


Theoretical massNumber of molelcules
Total (without water)23,7072
Polymers23,7072
Non-polymers00
Water6,323351
1
A: Beta-2-microglobulin
B: Beta-2-microglobulin

A: Beta-2-microglobulin
B: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)47,4134
Polymers47,4134
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)89.948, 89.948, 54.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is a dimer containing one of the copies in the asymmetric unit and its symmetry-mate generated by the operation: y, x, -z

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Components

#1: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11853.319 Da / Num. of mol.: 2 / Mutation: P32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 31% PEG 4000, 25% glycerol, 0.2M ammonium acetate, 0.1M sodium acetate; drops contained 1ul of ~19 mg/ml protein, 1ul of mother liquor, and 1ul of 0.05M sodium acetate pH 5.6, VAPOR ...Details: 31% PEG 4000, 25% glycerol, 0.2M ammonium acetate, 0.1M sodium acetate; drops contained 1ul of ~19 mg/ml protein, 1ul of mother liquor, and 1ul of 0.05M sodium acetate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9766 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 13, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9766 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 25244 / Num. obs: 25232 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.827 / % possible all: 99.6

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Phasing

Phasing dmFOM : 0.91 / FOM acentric: 0.91 / FOM centric: 0.93 / Reflection: 16403 / Reflection acentric: 13931 / Reflection centric: 2472
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.6-46.7360.930.930.94797507290
3.5-5.60.930.930.9422571785472
2.8-3.50.920.920.9427552317438
2.5-2.80.910.910.9227522376376
2.1-2.50.910.90.9148544280574
2-2.10.90.90.9129882666322

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RESOLVE2.09phasing
REFMAC5.2.0011refinement
PDB_EXTRACT1.701data extraction
CBASSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LDS

1lds


Resolution: 1.7→46.78 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.614 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22717 1288 5.1 %RANDOM
Rwork0.1838 ---
obs0.18587 23868 99.66 %-
all-25241 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.657 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.26 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1564 0 0 351 1915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221612
X-RAY DIFFRACTIONr_bond_other_d0.0070.021104
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9372186
X-RAY DIFFRACTIONr_angle_other_deg0.6743.0032674
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.395186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4724.04884
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.82115274
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.733158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
X-RAY DIFFRACTIONr_nbd_refined0.1840.2261
X-RAY DIFFRACTIONr_nbd_other0.1970.21047
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2778
X-RAY DIFFRACTIONr_nbtor_other0.0790.2830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1270.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1261252
X-RAY DIFFRACTIONr_mcbond_other0.7666372
X-RAY DIFFRACTIONr_mcangle_it3.77891534
X-RAY DIFFRACTIONr_scbond_it4.2526904
X-RAY DIFFRACTIONr_scangle_it5.2069652
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 92 -
Rwork0.263 1698 -
obs--98.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.897-0.83790.54320.9039-0.56491.2629-0.0157-0.0020.06130.1095-0.0637-0.0954-0.1454-0.06140.0795-0.04070.0018-0.0108-0.0578-0.0155-0.02333.191319.257912.4272
21.7748-0.2816-0.79341.44480.79171.25390.0731-0.28610.05160.075-0.0794-0.00530.1036-0.11570.0063-0.07760.0318-0.00070.0523-0.0423-0.094610.041316.409115.2179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 975 - 98
2X-RAY DIFFRACTION2BB4 - 975 - 98

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