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- PDB-7kpk: Crystal structure of the SPOP MATH domain in complex with a fragm... -

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Basic information

Entry
Database: PDB / ID: 7kpk
TitleCrystal structure of the SPOP MATH domain in complex with a fragment of Pdx1
Components
  • Pdx1 peptide
  • Speckle-type POZ protein
KeywordsGENE REGULATION / ubiquitin / ligase / adaptor / protein / diabetes / transcription factor
Function / homology
Function and homology information


protein catabolic process
Similarity search - Function
MATH domain / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / BTB/POZ domain / SKP1/BTB/POZ domain superfamily
Similarity search - Domain/homology
Speckle type BTB/POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsUsher, E.T. / Boal, A.K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK121509 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)F31DK124047 United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Intrinsically disordered substrates dictate SPOP subnuclear localization and ubiquitination activity.
Authors: Usher, E.T. / Sabri, N. / Rohac, R. / Boal, A.K. / Mittag, T. / Showalter, S.A.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
B: Pdx1 peptide


Theoretical massNumber of molelcules
Total (without water)18,4162
Polymers18,4162
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Purification by gel filtration ensured that SPOP-MATH existed as a monomer.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-4 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.796, 53.985, 41.556
Angle α, β, γ (deg.)90.000, 101.430, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-280-

HOH

21A-303-

HOH

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Components

#1: Protein Speckle-type POZ protein


Mass: 16352.821 Da / Num. of mol.: 1 / Fragment: MATH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / References: UniProt: D6RDG8
#2: Protein/peptide Pdx1 peptide


Mass: 2063.297 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.84 Å3/Da / Density % sol: 33.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium cacodylate, pH 6.5, 0.08 M magnesium acetate, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.7999898 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999898 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 13113 / % possible obs: 89.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.46 Å2 / CC1/2: 0.982 / Net I/σ(I): 20.5
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 684 / CC1/2: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IVB

3ivb


Resolution: 1.71→30.75 Å / SU ML: 0.1577 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 24.025
RfactorNum. reflection% reflection
Rfree0.2271 649 5.02 %
Rwork0.181 --
obs0.1835 12920 87.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.73 Å2
Refinement stepCycle: LAST / Resolution: 1.71→30.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 108 1238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141153
X-RAY DIFFRACTIONf_angle_d1.34991544
X-RAY DIFFRACTIONf_chiral_restr0.0915166
X-RAY DIFFRACTIONf_plane_restr0.01192
X-RAY DIFFRACTIONf_dihedral_angle_d10.3181696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.840.26371290.19952350X-RAY DIFFRACTION85.34
1.84-2.020.25811180.19122353X-RAY DIFFRACTION84.8
2.02-2.310.22451300.17782406X-RAY DIFFRACTION86.41
2.31-2.920.25891350.19352517X-RAY DIFFRACTION90.54
2.92-30.750.19671370.16922645X-RAY DIFFRACTION92.76

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