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

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Basic information

Entry
Database: PDB / ID: 3ivq
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-CiSBC2
Components
  • CiSBC2
  • Speckle-type POZ protein
KeywordsLIGASE / Protein Binding / Nucleus / Ubl conjugation pathway
Function / homology
Function and homology information


regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm ...regulation of proteolysis / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / localization / Hedgehog 'on' state / protein polyubiquitination / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SPOP, C-terminal 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. ...SPOP, C-terminal 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: 2.1 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

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Assembly

Deposited unit
A: Speckle-type POZ protein
C: CiSBC2
B: Speckle-type POZ protein
D: CiSBC2


Theoretical massNumber of molelcules
Total (without water)35,6994
Polymers35,6994
Non-polymers00
Water2,774154
1
A: Speckle-type POZ protein
C: CiSBC2


Theoretical massNumber of molelcules
Total (without water)17,8492
Polymers17,8492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-5 kcal/mol
Surface area7720 Å2
MethodPISA
2
B: Speckle-type POZ protein
D: CiSBC2


Theoretical massNumber of molelcules
Total (without water)17,8492
Polymers17,8492
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-6 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.703, 59.829, 151.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16543.967 Da / Num. of mol.: 2
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 CiSBC2


Mass: 1305.371 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.83 Å3/Da / Density % sol: 32.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 28% PME 550, 0.1 M BTP, Cryoprotection: 35% PME 550, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 15678 / Num. obs: 15674 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.077 / Net I/σ(I): 26
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 1558 / Rsym value: 0.365 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→40 Å / Isotropic thermal model: OVERALL ANISOTROPIC / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2789 754 RANDOM
Rwork0.2337 --
all0.245 15685 -
obs0.245 15629 -
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.028 Å20 Å20 Å2
2--0.777 Å20 Å2
3----1.804 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2339 0 0 154 2493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007993
X-RAY DIFFRACTIONc_angle_d1.69247

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