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- PDB-3ivb: Structures of SPOP-Substrate Complexes: Insights into Architectur... -

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Basic information

Entry
Database: PDB / ID: 3ivb
TitleStructures of SPOP-Substrate Complexes: Insights into Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATH-MacroH2ASBCpep1
Components
  • Core histone macro-H2A.1
  • Speckle-type POZ protein
Keywordsprotein binding / ligase / Protein Binding/Hydrolase / Nucleus / Ubl conjugation pathway / Alternative splicing / Chromatin regulator / Chromosomal protein / DNA-binding / Isopeptide bond / Methylation / Nucleosome core / Phosphoprotein / Ubl conjugation
Function / homology
Function and homology information


negative regulation of cell cycle G2/M phase transition / positive regulation of endodermal cell differentiation / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / Barr body / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding ...negative regulation of cell cycle G2/M phase transition / positive regulation of endodermal cell differentiation / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / Barr body / positive regulation of maintenance of mitotic sister chromatid cohesion / regulation of response to oxidative stress / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / regulation of oxidative phosphorylation / double-stranded methylated DNA binding / sex chromatin / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / rDNA binding / positive regulation of keratinocyte differentiation / dosage compensation by inactivation of X chromosome / poly-ADP-D-ribose modification-dependent protein binding / establishment of protein localization to chromatin / molecular function inhibitor activity / negative regulation of response to oxidative stress / Cul3-RING ubiquitin ligase complex / negative regulation of gene expression, epigenetic / nuclear chromosome / regulation of proteolysis / regulation of lipid metabolic process / protein serine/threonine kinase inhibitor activity / pericentric heterochromatin / condensed chromosome / transcription initiation-coupled chromatin remodeling / site of DNA damage / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / epigenetic regulation of gene expression / chromatin DNA binding / Hedgehog 'on' state / nucleosomal DNA binding / SPOP-mediated proteasomal degradation of PD-L1(CD274) / protein polyubiquitination / structural constituent of chromatin / nucleosome / nucleosome assembly / heterochromatin formation / proteasome-mediated ubiquitin-dependent protein catabolic process / chromosome, telomeric region / nuclear speck / transcription cis-regulatory region binding / protein heterodimerization activity / ubiquitin protein ligase binding / DNA repair / nucleolus / protein kinase binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSchulman, B.A. / Miller, D.J. / Calabrese, M.F. / Seyedin, S.
CitationJournal: To be Published
Title: Structure 9
Authors: Zhuang, M. / Calabrese, M.F. / Liu, J. / Waddell, M.B. / Nourse, A. / Hammel, M. / Miller, D.J. / Walden, H. / Duda, D.M. / Steven, S. / Hoggard, T. / Harper, J.W. / White, K.P. / Schulman, B.A.
History
DepositionAug 31, 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Speckle-type POZ protein
M: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3298
Polymers17,9662
Non-polymers3626
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.021, 44.021, 266.840
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 / HIB homolog 1 / Roadkill homolog 1


Mass: 16543.967 Da / Num. of mol.: 1 / Fragment: UNP residues 28-166
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 Core histone macro-H2A.1 / Histone macroH2A1 / mH2A1 / H2A.y / H2A/y / Medulloblastoma antigen MU-MB-50.205


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


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 10-20% PEG3350, 0.1 M Tris pH 7.6, 50 mM zinc acetate. Cryoprotection 30% PEG400, 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
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 16750 / Num. obs: 16414 / % possible obs: 98 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0
Reflection shellResolution: 1.75→1.81 Å / % possible all: 97.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→37.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.697 / SU ML: 0.083 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24729 828 5.1 %RANDOM
Rwork0.21827 ---
obs0.21964 15566 98.61 %-
all-15566 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.752 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→37.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 6 96 1307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221232
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9611663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.475155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96523.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.3515227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.457159
X-RAY DIFFRACTIONr_chiral_restr0.0840.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02920
X-RAY DIFFRACTIONr_nbd_refined0.2150.2541
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2844
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.293
X-RAY DIFFRACTIONr_metal_ion_refined0.1890.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.224
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1990.24
X-RAY DIFFRACTIONr_mcbond_it1.1331.5768
X-RAY DIFFRACTIONr_mcangle_it1.6421204
X-RAY DIFFRACTIONr_scbond_it2.9843529
X-RAY DIFFRACTIONr_scangle_it3.3344.5454
X-RAY DIFFRACTIONr_rigid_bond_restr3.03431297
X-RAY DIFFRACTIONr_sphericity_free4.9163102
X-RAY DIFFRACTIONr_sphericity_bonded1.98831205
LS refinement shellResolution: 1.75→1.797 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 57 -
Rwork0.253 1070 -
obs--96.74 %

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