[English] 日本語
Yorodumi
- PDB-1otr: Solution Structure of a CUE-Ubiquitin Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1otr
TitleSolution Structure of a CUE-Ubiquitin Complex
Components
  • Ubiquitin
  • protein Cue2
KeywordsCELL CYCLE / PROTEIN-PROTEIN COMPLEX
Function / homology
Function and homology information


: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) ...: / : / : / : / : / Regulation of TP53 Degradation / Josephin domain DUBs / RAS processing / Regulation of PTEN localization / ER Quality Control Compartment (ERQC) / UCH proteinases / Interleukin-1 signaling / Aggrephagy / Pexophagy / PINK1-PRKN Mediated Mitophagy / Regulation of pyruvate metabolism / nuclear-transcribed mRNA catabolic process, no-go decay / Peroxisomal protein import / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ABC-family proteins mediated transport / Metalloprotease DUBs / Endosomal Sorting Complex Required For Transport (ESCRT) / E3 ubiquitin ligases ubiquitinate target proteins / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Translesion Synthesis by POLH / Termination of translesion DNA synthesis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Negative regulators of DDX58/IFIH1 signaling / K63-linked polyubiquitin modification-dependent protein binding / Formation of the ternary complex, and subsequently, the 43S complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / Ribosomal scanning and start codon recognition / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Formation of TC-NER Pre-Incision Complex / Orc1 removal from chromatin / Major pathway of rRNA processing in the nucleolus and cytosol / MAPK6/MAPK4 signaling / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Gap-filling DNA repair synthesis and ligation in TC-NER / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / Antigen processing: Ubiquitination & Proteasome degradation / L13a-mediated translational silencing of Ceruloplasmin expression / Dual incision in TC-NER / ribosomal large subunit export from nucleus / polyubiquitin modification-dependent protein binding / Ub-specific processing proteases / cytosolic ribosome / rescue of stalled ribosome / RNA endonuclease activity / ubiquitin binding / modification-dependent protein catabolic process / protein tag activity / peroxisome / ribosome biogenesis / ribosomal large subunit assembly / endonuclease activity / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / structural constituent of ribosome / ubiquitin protein ligase binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-binding protein Cue2, CUE domain 1 / Ubiquitin-binding protein Cue2, CUE domain 2 / : / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE ...Ubiquitin-binding protein Cue2, CUE domain 1 / Ubiquitin-binding protein Cue2, CUE domain 2 / : / Small MutS-related domain / Smr domain superfamily / Smr domain / Smr domain profile. / CUE domain / Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs) / Ubiquitin system component CUE / CUE domain profile. / Ubiquitin-associated (UBA) domain / UBA-like superfamily / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / Helicase, Ruva Protein; domain 3 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Polyubiquitin / Endonuclease CUE2 / Ubiquitin-60S ribosomal protein L40
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
AuthorsKang, R.S. / Daniels, C.M. / Salerno, W.J. / Radhakrishnan, I.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2003
Title: Solution Structure of a CUE-Ubiquitin Complex Reveals a Conserved Mode of Ubiquitin Binding
Authors: Kang, R.S. / Daniels, C.M. / Francis, S.A. / Shih, S.C. / Salerno, W.J. / Hicke, L. / Radhakrishnan, I.
History
DepositionMar 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
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: protein Cue2
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)14,1422
Polymers14,1422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 80The submitted conformer models are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
RepresentativeModel #1closest to the average

-
Components

#1: Protein/peptide protein Cue2 / HYPOTHETICAL 50.9 KD PROTEIN IN BUD2-MIF2 INTERGENIC REGION / hypothetical protein YKL090w


Mass: 5573.291 Da / Num. of mol.: 1 / Fragment: Amino-terminal CUE Domain, Residues 6-54
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CUE2 / Plasmid: pMCSG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P36075
#2: Protein Ubiquitin


Mass: 8568.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBI1 / Plasmid: pET-3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61864, UniProt: P0CG63*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1333D 13C-filtered, 13C-edited NOESY
1442D DOUBLE HALF-FILTERED NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN390% H2O/10% D2O
21 mM U-15N,13C Cue2 + 1 mM Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN399.996% D2O
31 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN390% H2O/10% D2O
41 mM Cue2 + 1 mM U-15N,13C Ubiquitin; 20 mM sodium phosphate buffer, pH 7.0, 0.2% NaN399.996% D2O
Sample conditionsIonic strength: 20 mM sodium phosphate, pH 7.0, 0.2% NaN3 / pH: 7 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1bVariancollection
Felix98.0 and 2000Accelrysprocessing
Felix98.0 and 2000Accelrysdata analysis
CNS1.1Brunger et al.structure solution
ARIA1.2Linge and Nilgesstructure solution
ARIA1.2Linge and Nilgesrefinement
CNS1.1Brunger et al.refinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3328 distance restraints, including 3238 NOE-derived distance restraints [2560 unambiguous and 678 ambiguous restraints], 90 hydrogen bonding distance ...Details: The structures are based on a total of 3328 distance restraints, including 3238 NOE-derived distance restraints [2560 unambiguous and 678 ambiguous restraints], 90 hydrogen bonding distance restraints, and 150 torsion angle restraints.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: The submitted conformer models are the 20 structures with the lowest restraint energies, restraint violations, and RMS deviations from ideal covalent geometry
Conformers calculated total number: 80 / Conformers submitted total number: 20

+
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