[English] 日本語
Yorodumi
- PDB-3hsv: Structures of SPOP-Substrate Complexes: Insights into Molecular A... -

+
Open data


ID or keywords:

Loading...

-
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 / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding ...negative regulation of cell cycle G2/M phase transition / negative regulation of protein localization to chromosome, telomeric region / regulation of NAD metabolic process / positive regulation of response to oxidative stress / positive regulation of maintenance of mitotic sister chromatid cohesion / negative regulation of response to oxidative stress / regulation of response to oxidative stress / Barr body / ADP-D-ribose binding / ADP-D-ribose modification-dependent protein binding / sex-chromosome dosage compensation / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / sex chromatin / establishment of protein localization to chromatin / positive regulation of endodermal cell differentiation / double-stranded methylated DNA binding / rDNA binding / regulation of oxidative phosphorylation / negative regulation of protein serine/threonine kinase activity / regulation of proteolysis / poly-ADP-D-ribose modification-dependent protein binding / protein serine/threonine kinase inhibitor activity / positive regulation of keratinocyte differentiation / nucleosomal DNA binding / negative regulation of gene expression, epigenetic / Cul3-RING ubiquitin ligase complex / nuclear chromosome / molecular function inhibitor activity / site of DNA damage / regulation of lipid metabolic process / localization / pericentric heterochromatin / epigenetic regulation of gene expression / condensed chromosome / transcription initiation-coupled chromatin remodeling / promoter-specific chromatin binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hedgehog 'on' state / chromatin DNA binding / nucleosome assembly / protein polyubiquitination / structural constituent of chromatin / nucleosome / 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 / chromatin / nucleolus / protein kinase binding / negative regulation of transcription by RNA polymerase II / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Core histone macro-H2A / Core histone macro-H2A, macro domain / SPOP, C-terminal 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 ...Core histone macro-H2A / Core histone macro-H2A, macro domain / SPOP, C-terminal 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 H2A / Histone 2A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Sulfate


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.55 %

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more