[English] 日本語
Yorodumi
- PDB-1u9b: MURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u9b
TitleMURINE/HUMAN UBIQUITIN-CONJUGATING ENZYME UBC9
ComponentsUBIQUITIN-CONJUGATING ENZYME E9
KeywordsLIGASE / UBIQUITIN-CONJUGATING ENZYME / UBIQUITIN-DIRECTED PROTEOLYSIS / CELL CYCLE CONTROL
Function / homology
Function and homology information


SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins ...SUMO is transferred from E1 to E2 (UBE2I, UBC9) / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / SUMOylation of nuclear envelope proteins / Vitamin D (calciferol) metabolism / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of ubiquitinylation proteins / SUMOylation of SUMOylation proteins / SUMOylation of DNA replication proteins / SUMOylation of transcription factors / SUMOylation of RNA binding proteins / SUMOylation of DNA methylation proteins / SUMOylation of DNA damage response and repair proteins / SUMOylation of transcription cofactors / SUMOylation of chromatin organization proteins / SUMOylation of intracellular receptors / SUMOylation of immune response proteins / Formation of Incision Complex in GG-NER / SUMO conjugating enzyme activity / Processing of DNA double-strand break ends / Transcriptional and post-translational regulation of MITF-M expression and activity / RING-like zinc finger domain binding / SUMO ligase complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / HLH domain binding / small protein activating enzyme binding / nuclear export / Transferases; Acyltransferases; Aminoacyltransferases / protein sumoylation / postsynaptic cytosol / nuclear pore / presynaptic cytosol / transcription coregulator binding / chromosome segregation / PML body / modulation of chemical synaptic transmission / protein modification process / Schaffer collateral - CA1 synapse / positive regulation of canonical NF-kappaB signal transduction / nuclear body / positive regulation of cell migration / cell division / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like ...: / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTong, H. / Hateboer, G. / Perrakis, A. / Bernards, R. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 1997
Title: Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system.
Authors: Tong, H. / Hateboer, G. / Perrakis, A. / Bernards, R. / Sixma, T.K.
History
DepositionMay 20, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UBIQUITIN-CONJUGATING ENZYME E9


Theoretical massNumber of molelcules
Total (without water)18,2581
Polymers18,2581
Non-polymers00
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.390, 93.950, 115.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein UBIQUITIN-CONJUGATING ENZYME E9 / UBC9


Mass: 18258.076 Da / Num. of mol.: 1 / Mutation: INS(ASN 0)
Source method: isolated from a genetically manipulated source
Details: MAMMALIAN / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P63280, ubiquitin-protein ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.64 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.5
Details: 23% PEG MONOMETHYL ETHER 5000,9% ISOPROPANOL, 0.1 M AMMONIUM SULFATE, 0.1 M MES BUFFER, PH6.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15.5 mg/mlprotein1drop
275 mM1dropNaCl
30.25 mMdithiothreitol1drop
45 mMHEPES1drop
511.5 %PEG50001drop
64.5 %isopropanol1drop
70.05 Mammonium sulfate1drop
80.05 MMES1drop
923 %PEG50001reservoir
109 %isopropanol1reservoir
110.1 Mammonium sulfate1reservoir
120.1 MMES1reservoir

-
Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.885
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 26, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.885 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 12854 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 17
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3 / Rsym value: 0.41 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AAK

1aak
PDB Unreleased entry


Resolution: 2→10 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.25 629 5 %RANDOM
Rwork0.185 ---
all-12854 --
obs-12854 98 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 228.3 Å2 / ksol: 0.8 e/Å3
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 0 96 1372
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01513130.5
X-RAY DIFFRACTIONt_angle_deg1.4417643
X-RAY DIFFRACTIONt_dihedral_angle_d16.77690
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.006342
X-RAY DIFFRACTIONt_gen_planes0.0121845
X-RAY DIFFRACTIONt_it2.6413133
X-RAY DIFFRACTIONt_nbd0.0111310
Software
*PLUS
Name: TNT / Version: 5D / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185 / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0062
X-RAY DIFFRACTIONt_plane_restr0.0125
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.70

+
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