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- PDB-6f8g: Co-crystal structure of SPOP MATH domain and hamster Pdx1 fragment -

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Basic information

Entry
Database: PDB / ID: 6f8g
TitleCo-crystal structure of SPOP MATH domain and hamster Pdx1 fragment
Components
  • Pancreas/duodenum homeobox protein 1
  • Speckle-type POZ protein
KeywordsLIGASE / Nuclear / Diabetes
Function / homology
Function and homology information


type B pancreatic cell differentiation / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of proteolysis / Hedgehog 'on' state / positive regulation of insulin secretion / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck ...type B pancreatic cell differentiation / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of proteolysis / Hedgehog 'on' state / positive regulation of insulin secretion / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / ubiquitin protein ligase binding / 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)
Mesocricetus auratus (golden hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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: Speckle-type POZ protein
C: Speckle-type POZ protein
D: Speckle-type POZ protein
E: Pancreas/duodenum homeobox protein 1
F: Pancreas/duodenum homeobox protein 1
G: Pancreas/duodenum homeobox protein 1
H: Pancreas/duodenum homeobox protein 1


Theoretical massNumber of molelcules
Total (without water)71,4578
Polymers71,4578
Non-polymers00
Water6,359353
1
A: Speckle-type POZ protein
B: Speckle-type POZ protein
E: Pancreas/duodenum homeobox protein 1
H: Pancreas/duodenum homeobox protein 1


Theoretical massNumber of molelcules
Total (without water)35,7294
Polymers35,7294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-17 kcal/mol
Surface area14060 Å2
MethodPISA
2
D: Speckle-type POZ protein
G: Pancreas/duodenum homeobox protein 1

C: Speckle-type POZ protein
F: Pancreas/duodenum homeobox protein 1


Theoretical massNumber of molelcules
Total (without water)35,7294
Polymers35,7294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
MethodPISA
3
C: Speckle-type POZ protein
F: Pancreas/duodenum homeobox protein 1

D: Speckle-type POZ protein
G: Pancreas/duodenum homeobox protein 1


Theoretical massNumber of molelcules
Total (without water)35,7294
Polymers35,7294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4210 Å2
ΔGint-21 kcal/mol
Surface area14190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.400, 55.170, 58.070
Angle α, β, γ (deg.)89.25, 89.89, 86.76
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 16616.137 Da / Num. of mol.: 4
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 / Homeodomain protein PDX1 / Insulin promoter factor 1 / IPF-1


Mass: 1248.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mesocricetus auratus (golden hamster) / References: UniProt: P70118
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Imidazole-HCl pH 8.0, 30% (w/v) MPD, 10% (w/v) PEG-4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.03→100 Å / Num. all: 124076 / Num. obs: 32906 / % possible obs: 96.4 % / Redundancy: 3.54 % / Rrim(I) all: 0.106 / Net I/σ(I): 8.62
Reflection shellResolution: 2.05→2.102 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: 2.03→19.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.358 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.217 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26169 1650 4.8 %RANDOM
Rwork0.18414 ---
obs0.18806 32906 97.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.798 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å2-0.01 Å2
2--0 Å20.02 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.03→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4760 0 0 353 5113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024892
X-RAY DIFFRACTIONr_bond_other_d0.0020.024566
X-RAY DIFFRACTIONr_angle_refined_deg1.6931.9596575
X-RAY DIFFRACTIONr_angle_other_deg1.003310589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7175609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.65824.151212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88115891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6191525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021058
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_it3.1663.8062430
X-RAY DIFFRACTIONr_mcbond_other3.1673.8052429
X-RAY DIFFRACTIONr_mcangle_it4.7155.6873026
X-RAY DIFFRACTIONr_mcangle_other4.7145.6883027
X-RAY DIFFRACTIONr_scbond_it3.4214.0472462
X-RAY DIFFRACTIONr_scbond_other3.424.0482463
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2845.9313545
X-RAY DIFFRACTIONr_long_range_B_refined7.89344.8415379
X-RAY DIFFRACTIONr_long_range_B_other7.84944.6475335
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 119 -
Rwork0.309 2359 -
obs--97.33 %

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