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

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Basic information

Entry
Database: PDB / ID: 3hqh
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep1
Components
  • MacroH2A
  • Speckle-type POZ protein
KeywordsLIGASE / ubiquitin / SPOP / BTB / E3 / Nucleus / Ubl conjugation pathway
Function / homology
Function and homology information


Hedgehog 'on' state / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / positive regulation of response to oxidative stress / regulation of NAD metabolic process / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / negative regulation of protein serine/threonine kinase activity / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding ...Hedgehog 'on' state / negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / positive regulation of response to oxidative stress / regulation of NAD metabolic process / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / negative regulation of protein serine/threonine kinase activity / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex-chromosome dosage compensation / positive regulation of endodermal cell differentiation / double-stranded methylated DNA binding / establishment of protein localization to chromatin / regulation of oxidative phosphorylation / sex chromatin / Barr body / rDNA binding / poly-ADP-D-ribose modification-dependent protein binding / positive regulation of keratinocyte differentiation / negative regulation of response to oxidative stress / nucleosomal DNA binding / molecular function inhibitor activity / Cul3-RING ubiquitin ligase complex / nuclear chromosome / negative regulation of gene expression, epigenetic / regulation of lipid metabolic process / regulation of proteolysis / site of DNA damage / protein serine/threonine kinase inhibitor activity / pericentric heterochromatin / condensed chromosome / transcription initiation-coupled chromatin remodeling / epigenetic regulation of gene expression / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / Hedgehog 'on' state / chromatin DNA binding / protein polyubiquitination / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / transcription cis-regulatory region binding / nuclear speck / protein ubiquitination / protein heterodimerization activity / DNA repair / ubiquitin protein ligase binding / protein kinase binding / chromatin / nucleolus / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / 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 ...Core histone macro-H2A / Core histone macro-H2A, macro domain / 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 / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Speckle-type POZ protein / Core histone macro-H2A.1 / Speckle-type POZ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Revision 1.4Sep 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
M: MacroH2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1055
Polymers17,9082
Non-polymers1963
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-43 kcal/mol
Surface area7090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.700, 44.700, 268.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Speckle-type POZ protein


Mass: 16485.932 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: Q6P8B3, UniProt: O43791*PLUS
#2: Protein/peptide MacroH2A


Mass: 1422.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: O75367*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% PEG550, 0.1M MES 6.5, 20mM ZnSO4 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. all: 8052 / Num. obs: 8052 / Observed criterion σ(F): 0 / Observed criterion σ(I): 8.3 / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 31.7
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 8.3 / Rsym value: 0.182

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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 entry 2cr2.pdb

2cr2


Resolution: 2.3→50 Å / Cross valid method: Rfree / σ(F): 0 / σ(I): 8.3
RfactorNum. reflection% reflectionSelection details
Rfree0.276 360 -random
Rwork0.238 ---
obs0.2568 7805 99.1 %-
all-7873 --
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 3 48 1181

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