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

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Basic information

Entry
Database: PDB / ID: 3hql
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases:SPOPMATHx-PucSBC1_pep2
Components
  • Puckered
  • Speckle-type POZ protein
KeywordsProtein Binding / Ligase/Hydrolase / ubiquitin / E3 / SPOP / Puckered / MATH / Nucleus / Ubl conjugation pathway / Hydrolase / Ligase-Hydrolase COMPLEX
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 / negative regulation of stress-activated protein kinase signaling cascade ...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 / negative regulation of stress-activated protein kinase signaling cascade / determination of digestive tract left/right asymmetry / Negative regulation of MAPK pathway / negative regulation of peptidoglycan recognition protein signaling pathway / dorsal closure / follicle cell of egg chamber development / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine phosphatase activity / dorsal appendage formation / compound eye development / positive regulation of border follicle cell migration / MAP kinase tyrosine/serine/threonine phosphatase activity / negative regulation of programmed cell death / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / histone H2AXS140 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / calmodulin-dependent protein phosphatase activity / myosin phosphatase activity / phosphoprotein phosphatase activity / protein secretion / regulation of proteolysis / negative regulation of tumor necrosis factor-mediated signaling pathway / epidermis development / negative regulation of MAPK cascade / JNK cascade / regulation of G2/M transition of mitotic cell cycle / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / determination of adult lifespan / wound healing / Hedgehog 'on' state / positive regulation of immune response / protein polyubiquitination / actin cytoskeleton organization / cellular response to oxidative stress / response to oxidative stress / proteasome-mediated ubiquitin-dependent protein catabolic process / nuclear speck / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / signal transduction / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
SPOP, C-terminal BACK domain / : / MATH 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 / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain ...SPOP, C-terminal BACK domain / : / MATH 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 / 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 / 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 / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / SKP1/BTB/POZ domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 7, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,4536
Polymers36,2614
Non-polymers1922
Water4,972276
1
A: Speckle-type POZ protein
C: Puckered
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2273
Polymers18,1312
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-15 kcal/mol
Surface area7290 Å2
MethodPISA
2
B: Speckle-type POZ protein
D: Puckered
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2273
Polymers18,1312
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-14 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.795, 43.690, 86.819
Angle α, β, γ (deg.)90.00, 107.03, 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: 16485.932 Da / Num. of mol.: 2 / Fragment: UNP residues 28-166 / 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: 1644.669 Da / Num. of mol.: 2 / Fragment: UNP residues 91-106 / Source method: obtained synthetically
References: UniProt: Q9VHV8, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.66→20 Å / Num. obs: 38876 / Observed criterion σ(F): 0 / Redundancy: 3.1 % / Rsym value: 0.073 / Net I/σ(I): 28.9
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3796 / Rsym value: 0.39

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HQH

3hqh


Resolution: 1.66→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.699 / SU ML: 0.079 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25806 1934 5 %RANDOM
Rwork0.24659 ---
obs0.24721 36636 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.41 Å2
2---0.74 Å20 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.66→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2168 0 10 276 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222257
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9573035
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.915284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15922.52791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74115394
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3941516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2333
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021658
X-RAY DIFFRACTIONr_nbd_refined0.1980.2925
X-RAY DIFFRACTIONr_nbtor_refined0.310.21560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2670.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.225
X-RAY DIFFRACTIONr_mcbond_it1.2351.51445
X-RAY DIFFRACTIONr_mcangle_it1.70622221
X-RAY DIFFRACTIONr_scbond_it2.7073946
X-RAY DIFFRACTIONr_scangle_it4.1234.5812
LS refinement shellResolution: 1.66→1.72 Å / Num. reflection Rwork: 2517 / Total num. of bins used: 20
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.54650.28180.06911.23710.09681.1307-0.03340.1046-0.0104-0.13240.0383-0.14660.0009-0.0406-0.0049-0.0748-0.011-0.0002-0.0163-0.0053-0.01990.564-0.03736.38
21.6931-0.34490.08141.314-0.02861.1269-0.0294-0.1181-0.01020.14450.040.15510.00740.0449-0.0106-0.07350.00860.0011-0.01230.0059-0.025-13.277-21.7825.095
310.20671.8431-1.118515.85890.94024.0063-0.13550.73380.0418-0.0193-0.2313-0.3554-0.27480.13780.3668-0.0422-0.0574-0.03010.10640.0737-0.21832.6444.36826.015
412.60779.96450.525816.97272.40177.1935-0.1098-0.69470.85-0.16250.07261.0238-0.055-0.16530.0372-0.13430.090.07210.0481-0.0179-0.0228-15.176-17.98115.894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 164
2X-RAY DIFFRACTION2B28 - 164
3X-RAY DIFFRACTION3C95 - 102
4X-RAY DIFFRACTION4D96 - 102

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