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- PDB-6f8f: Co-crystal structure of SPOP MATH domain and human Pdx1 fragment -

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Basic information

Entry
Database: PDB / ID: 6f8f
TitleCo-crystal structure of SPOP MATH domain and human Pdx1 fragment
Components
  • Pancreas/duodenum homeobox protein 1
  • Speckle-type POZ protein
KeywordsLIGASE / Nuclear / Diabetes
Function / homology
Function and homology information


response to vitamin / negative regulation of type B pancreatic cell apoptotic process / type B pancreatic cell differentiation / positive regulation of type B pancreatic cell proliferation / transdifferentiation / Regulation of gene expression in early pancreatic precursor cells / response to chlorate / glucose mediated signaling pathway / morphogenesis of embryonic epithelium / type B pancreatic cell apoptotic process ...response to vitamin / negative regulation of type B pancreatic cell apoptotic process / type B pancreatic cell differentiation / positive regulation of type B pancreatic cell proliferation / transdifferentiation / Regulation of gene expression in early pancreatic precursor cells / response to chlorate / glucose mediated signaling pathway / morphogenesis of embryonic epithelium / type B pancreatic cell apoptotic process / response to L-leucine / response to fatty acid / type B pancreatic cell proliferation / exocrine pancreas development / response to alkaloid / digestive tract development / insulin secretion / response to iron(II) ion / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / smoothened signaling pathway / Regulation of gene expression in beta cells / positive regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of proteolysis / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / animal organ regeneration / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / response to glucocorticoid / response to cytokine / liver development / animal organ morphogenesis / generation of precursor metabolites and energy / stem cell differentiation / response to nicotine / promoter-specific chromatin binding / Hedgehog 'on' state / positive regulation of insulin secretion / glucose metabolic process / protein polyubiquitination / negative regulation of epithelial cell proliferation / sequence-specific double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Homeobox protein, antennapedia type / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Homeobox domain, metazoa / MATH domain / MATH/TRAF domain ...Homeobox protein, antennapedia type / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Homeobox domain, metazoa / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Homeobox-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Pancreas/duodenum homeobox protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOstertag, M.S. / Popowicz, G.M. / Sattler, M.
CitationJournal: Structure / Year: 2019
Title: The Structure of the SPOP-Pdx1 Interface Reveals Insights into the Phosphorylation-Dependent Binding Regulation.
Authors: Ostertag, M.S. / Messias, A.C. / Sattler, M. / Popowicz, G.M.
History
DepositionDec 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
D: Speckle-type POZ protein
G: Pancreas/duodenum homeobox protein 1


Theoretical massNumber of molelcules
Total (without water)17,7512
Polymers17,7512
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-4 kcal/mol
Surface area7590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.925, 53.925, 207.410
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Speckle-type POZ protein / HIB homolog 1 / Roadkill homolog 1


Mass: 16616.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: O43791
#2: Protein/peptide Pancreas/duodenum homeobox protein 1 / PDX-1 / Glucose-sensitive factor / GSF / Insulin promoter factor 1 / IPF-1 / Insulin upstream ...PDX-1 / Glucose-sensitive factor / GSF / Insulin promoter factor 1 / IPF-1 / Insulin upstream factor 1 / IUF-1 / Islet/duodenum homeobox-1 / IDX-1 / Somatostatin-transactivating factor 1 / STF-1


Mass: 1135.159 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P52945
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.45 Å3/Da / Density % sol: 49.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M HEPES pH 6.5, 10% (w/v) PEG6000 (final pH 7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.82655 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82655 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 13193 / % possible obs: 99 % / Redundancy: 8.96 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 26.23
Reflection shellResolution: 2→2.051 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVV

3ivv


Resolution: 2→19.94 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.211 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27433 640 5 %RANDOM
Rwork0.21549 ---
obs0.21841 12184 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.815 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 35 1191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021179
X-RAY DIFFRACTIONr_bond_other_d0.0020.021080
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9561587
X-RAY DIFFRACTIONr_angle_other_deg1.01732497
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6055145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29123.96253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33615206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.567157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02259
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_it5.3836.095586
X-RAY DIFFRACTIONr_mcbond_other5.3436.093585
X-RAY DIFFRACTIONr_mcangle_it7.2959.101729
X-RAY DIFFRACTIONr_mcangle_other7.2919.103730
X-RAY DIFFRACTIONr_scbond_it5.8346.362593
X-RAY DIFFRACTIONr_scbond_other5.8296.364594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.4049.356859
X-RAY DIFFRACTIONr_long_range_B_refined10.99969.261273
X-RAY DIFFRACTIONr_long_range_B_other11.00169.1471271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 42 -
Rwork0.414 846 -
obs--98.01 %

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