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- PDB-3hu6: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -

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Basic information

Entry
Database: PDB / ID: 3hu6
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx/BTB/3-box-PucSBC1
Components
  • Puckered
  • Speckle-type POZ protein
KeywordsProtein Binding / Ligase / ubiquitin / E3 / SPOP / Puckered / Nucleus / Ubl conjugation pathway / Hydrolase
Function / homology
Function and homology information


imaginal disc eversion / imaginal disc fusion / RAF-independent MAPK1/3 activation / chorion micropyle formation / embryonic anterior midgut (ectodermal) morphogenesis / imaginal disc fusion, thorax closure / JUN kinase phosphatase activity / chitin-based embryonic cuticle biosynthetic process / imaginal disc-derived male genitalia morphogenesis / determination of digestive tract left/right asymmetry ...imaginal disc eversion / imaginal disc fusion / RAF-independent MAPK1/3 activation / chorion micropyle formation / embryonic anterior midgut (ectodermal) morphogenesis / imaginal disc fusion, thorax closure / JUN kinase phosphatase activity / chitin-based embryonic cuticle biosynthetic process / imaginal disc-derived male genitalia morphogenesis / determination of digestive tract left/right asymmetry / negative regulation of stress-activated protein kinase signaling cascade / Negative regulation of MAPK pathway / negative regulation of peptidoglycan recognition protein signaling pathway / dorsal closure / follicle cell of egg chamber development / dorsal appendage formation / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / positive regulation of border follicle cell migration / compound eye development / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of proteolysis / negative regulation of programmed cell death / Cul3-RING ubiquitin ligase complex / molecular function inhibitor activity / myosin phosphatase activity / protein-serine/threonine phosphatase / phosphoprotein phosphatase activity / negative regulation of tumor necrosis factor-mediated signaling pathway / protein secretion / epidermis development / negative regulation of MAPK cascade / JNK cascade / regulation of G2/M transition of mitotic cell cycle / protein-tyrosine-phosphatase / determination of adult lifespan / wound healing / Hedgehog 'on' state / protein polyubiquitination / positive regulation of immune response / cellular response to oxidative stress / actin cytoskeleton organization / proteasome-mediated ubiquitin-dependent protein catabolic process / response to oxidative stress / nuclear speck / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SPOP, C-terminal BACK domain / MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / MATH/TRAF domain / MATH/TRAF domain profile. ...SPOP, C-terminal BACK domain / MATH domain / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A / MATH domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / TRAF-like / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / SKP1/BTB/POZ domain superfamily / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Puckered, isoform A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsZhuang, M. / Schulman, B.A.
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
DepositionJun 13, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,9604
Polymers71,9604
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-33 kcal/mol
Surface area29610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.740, 107.740, 130.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 35228.309 Da / Num. of mol.: 2 / Fragment: UNP residues 28-329 / Mutation: D140G
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 Puckered / SD08157p


Mass: 751.737 Da / Num. of mol.: 2 / Fragment: UNP residues 96-102 / Source method: obtained synthetically
References: UniProt: Q9VHV8, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / 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: 3.12 Å3/Da / Density % sol: 60.6 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDate: Jul 31, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 25440 / Observed criterion σ(F): 0 / Redundancy: 9.4 % / Rsym value: 0.174 / Net I/σ(I): 20.1
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 1877 / Rsym value: 0.59

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3HQH, 3HTM

3hqh

3htm


Resolution: 2.7→50 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2964 --random
Rwork0.2396 ---
all-24894 --
obs-23411 94 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--34.401 Å20 Å20 Å2
2--7.297 Å20 Å2
3---27.104 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4536 0 0 154 4690

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