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

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Basic information

Entry
Database: PDB / ID: 3hsv
TitleStructures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases: SPOPMATHx-MacroH2ASBCpep2
Components
  • Core histone macro-H2A.1
  • Speckle-type POZ protein
Keywordsprotein binding / ligase / ubiquitin / E3 / SPOP / MacroH2A / 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 / 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 ...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 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: 1.43 Å
AuthorsZhuang, M. / Schulman, B.A. / Miller, D.
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 10, 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 19, 2020Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_struct_special_symmetry / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity.src_method ..._entity.pdbx_fragment / _entity.src_method / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
M: Core histone macro-H2A.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8017
Polymers34,5083
Non-polymers2924
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-60 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.953, 43.086, 87.453
Angle α, β, γ (deg.)90.00, 118.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

21B-408-

HOH

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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 / Mutation: D140G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPOP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43791, UniProt: Q5NVK7*PLUS
#2: Protein/peptide Core histone macro-H2A.1 / mH2A1 / Histone H2A.y / H2A/y / Medulloblastoma antigen MU-MB-50.205


Mass: 1536.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75367
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.14 Å3/Da / Density % sol: 42.55 %

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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: 1.43→50 Å / Num. obs: 54191 / Observed criterion σ(F): 0 / Redundancy: 4.3 % / Rsym value: 0.057 / Net I/σ(I): 31.7
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 14.8 / Num. unique all: 5266 / Rsym value: 0.11

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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 2CR2

2cr2


Resolution: 1.43→31.23 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.875 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20576 2740 5.1 %RANDOM
Rwork0.17364 ---
obs0.17528 51030 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.43→31.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 10 404 2740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9683229
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0375305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.41323.679106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98115456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9791515
X-RAY DIFFRACTIONr_chiral_restr0.0820.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.21059
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21646
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2299
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.050.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0981.51486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.61722322
X-RAY DIFFRACTIONr_scbond_it2.19431043
X-RAY DIFFRACTIONr_scangle_it3.1244.5893
X-RAY DIFFRACTIONr_rigid_bond_restr1.17132529
X-RAY DIFFRACTIONr_sphericity_free3.3673412
X-RAY DIFFRACTIONr_sphericity_bonded2.30332331
LS refinement shellResolution: 1.43→1.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 174 -
Rwork0.155 3694 -
obs--98.37 %
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)
10.67570.0995-0.2980.6439-0.38021.0383-0.0219-0.0451-0.021-0.0414-0.01220.02280.01690.04630.0341-0.0271-0.003-0.0026-0.0251-0.001-0.017811.51420.81933.631
20.741-0.165-0.05670.46140.05540.8691-0.0062-0.01090.00580.0195-0.0024-0.00110.0032-0.04880.0086-0.0255-0.0042-0.0009-0.0253-0.0023-0.012713.04439.314.667
30.13410.4795-0.58538.212-6.45065.4773-0.05970.13090.0063-0.31830.26690.04530.3283-0.3139-0.20720.0597-0.0291-0.02160.04140.00760.00789.90125.64717.546
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 165
2X-RAY DIFFRACTION2B28 - 164
3X-RAY DIFFRACTION3M170 - 181

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