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- PDB-3ivv: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -

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Basic information

Entry
Database: PDB / ID: 3ivv
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-PucSBC1_pep1
Components
  • PucSBC1
  • Speckle-type POZ protein
KeywordsLIGASE / Protein Binding / Nucleus / Ubl conjugation pathway
Function / homology
Function and homology information


molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of proteolysis / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding ...molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / regulation of proteolysis / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
MATH domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology ...MATH domain / SPOP, C-terminal BACK domain / : / BPM/SPOP, BACK domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSchulman, B.A. / Miller, D.J. / Calabrese, M.F. / Seyedin, S.
CitationJournal: Mol.Cell / Year: 2009
Title: Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases.
Authors: Zhuang, M. / Calabrese, M.F. / Liu, J. / Waddell, M.B. / Nourse, A. / Hammel, M. / Miller, D.J. / Walden, H. / Duda, D.M. / Seyedin, S.N. / Hoggard, T. / Harper, J.W. / White, K.P. / Schulman, B.A.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
D: PucSBC1


Theoretical massNumber of molelcules
Total (without water)17,5572
Polymers17,5572
Non-polymers00
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.744, 56.492, 42.133
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16543.967 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 PucSBC1


Mass: 1012.970 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% PME 550, 0.1 M HEPES, Cryoprotection: 30% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 39304 / Num. obs: 39299 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rsym value: 0.038 / Net I/σ(I): 21.7
Reflection shellResolution: 1.25→1.29 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3926 / Rsym value: 0.276 / % possible all: 99.9

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→41.27 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.392 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19855 1976 5 %RANDOM
Rwork0.17677 ---
all0.18 37321 --
obs0.18 37321 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.867 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 0 0 216 1502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221325
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9721804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7975180
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11523.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.68315255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.886158
X-RAY DIFFRACTIONr_chiral_restr0.080.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02991
X-RAY DIFFRACTIONr_nbd_refined0.1930.2606
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2911
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2183
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.242
X-RAY DIFFRACTIONr_mcbond_it1.0021.5834
X-RAY DIFFRACTIONr_mcangle_it1.57521323
X-RAY DIFFRACTIONr_scbond_it2.6933556
X-RAY DIFFRACTIONr_scangle_it3.164.5467
X-RAY DIFFRACTIONr_rigid_bond_restr2.49431390
X-RAY DIFFRACTIONr_sphericity_free2.9063218
X-RAY DIFFRACTIONr_sphericity_bonded2.69731287
LS refinement shellResolution: 1.25→1.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 160 -
Rwork0.214 2685 -
obs--97.57 %

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