[English] 日本語
Yorodumi
- PDB-2lwx: Solution structure of the C-terminal Pdr1-activating domain of th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lwx
TitleSolution structure of the C-terminal Pdr1-activating domain of the J-protein Zuo1
ComponentsZuotin
KeywordsCHAPERONE / J-PROTEIN / MOLECULAR CHAPERONE / PLEIOTROPIC DRUG RESISTANCE
Function / homology
Function and homology information


translational frameshifting / 'de novo' cotranslational protein folding / Regulation of HSF1-mediated heat shock response / protein folding chaperone complex / regulation of translational fidelity / ribosomal subunit export from nucleus / Hsp70 protein binding / rRNA processing / protein folding / ribosome binding ...translational frameshifting / 'de novo' cotranslational protein folding / Regulation of HSF1-mediated heat shock response / protein folding chaperone complex / regulation of translational fidelity / ribosomal subunit export from nucleus / Hsp70 protein binding / rRNA processing / protein folding / ribosome binding / transcription coactivator activity / ribosome / intracellular signal transduction / nucleolus / mitochondrion / DNA binding / cytoplasm / cytosol
Similarity search - Function
Ribosome-associated complex head domain / Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. ...Ribosome-associated complex head domain / Ribosome-associated complex head domain / Ribosome-associated complex head domain superfamily / J-protein Zuotin/DnaJC2 / Ribosome-associated complex head domain / Nt-dnaJ domain signature. / DnaJ domain, conserved site / DnaJ domain / DnaJ molecular chaperone homology domain / dnaJ domain profile. / Chaperone J-domain superfamily / DnaJ domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsVolkman, B.F. / Ducett, J.K. / Peterson, F.C. / Craig, E.A.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Unfolding of the C-terminal domain of the j-protein zuo1 releases autoinhibition and activates pdr1-dependent transcription.
Authors: Ducett, J.K. / Peterson, F.C. / Hoover, L.A. / Prunuske, A.J. / Volkman, B.F. / Craig, E.A.
History
DepositionAug 8, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zuotin


Theoretical massNumber of molelcules
Total (without water)11,8361
Polymers11,8361
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 / 100target function
RepresentativeModel #1lowest energy

-
Components

#1: Protein Zuotin / DnaJ-related protein ZUO1 / J protein ZUO1 / Heat shock protein 40 homolog ZUO1 / Ribosome- ...DnaJ-related protein ZUO1 / J protein ZUO1 / Heat shock protein 40 homolog ZUO1 / Ribosome-associated complex subunit ZUO1


Mass: 11836.213 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PDR1 ACTIVATING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: YGR285C, ZUO1 / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21[PREP4] / References: UniProt: P32527

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1213D 13C- SEPARATED NOESY
1313D 13C- SEPARATED NOESY (AROMATIC)

-
Sample preparation

DetailsContents: 1.2 mM [U-100% 13C; U-100% 15N] ZUOTIN, 20 mM potassium phosphate, 50 mM sodium chloride, 1 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMZUOTIN-1[U-100% 13C; U-100% 15N]1
20 mMpotassium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
Sample conditionsIonic strength: 70 / pH: 6.5 / Pressure: AMBIENT / Temperature: 283 K

-
NMR measurement

NMR spectrometerType: BRUKER AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XPLOR-NIH2.9.3SCHWIETERS,C.D.,KUSZEWSKI,J.J.,TJrefinement
TopSpin2.1Bruker Biospincollection
NMRPipe2007Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASY1.3Bartels et al.data analysis
GARANT2.1Bartels, Guntert, Billeter and Wuthrichdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE ...Details: AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT. STRUCTURES ARE BASED ON A TOTAL OF 1471 NOE CONSTRAINTS (418 INTRA, 272 SEQUENTIAL, 463 MEDIUM, AND 318 LONG RANGE) AND 148 PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS.
NMR constraintsNOE constraints total: 1471 / NOE intraresidue total count: 418 / NOE long range total count: 318 / NOE medium range total count: 463 / NOE sequential total count: 272 / Protein phi angle constraints total count: 74 / Protein psi angle constraints total count: 74
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / 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://pdbjlvh1.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