[English] 日本語
Yorodumi
- PDB-2lwp: The NMR solution structure of the the ubiquitin homology domain o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2lwp
TitleThe NMR solution structure of the the ubiquitin homology domain of mouse BAG-1
ComponentsBAG family molecular chaperone regulator 1
KeywordsAPOPTOSIS / proteasomal degradation
Function / homology
Function and homology information


Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / positive regulation of smooth muscle cell apoptotic process / protein localization to mitochondrion / negative regulation of motor neuron apoptotic process / phosphoprotein binding / neuron differentiation / positive regulation of neuron apoptotic process / protein-folding chaperone binding / apoptotic process ...Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / positive regulation of smooth muscle cell apoptotic process / protein localization to mitochondrion / negative regulation of motor neuron apoptotic process / phosphoprotein binding / neuron differentiation / positive regulation of neuron apoptotic process / protein-folding chaperone binding / apoptotic process / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm / cytosol
Similarity search - Function
Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues ...Molecular chaperone regulator BAG / BAG domain superfamily / BAG domain / BAG domain / BAG domain profile. / BAG domains, present in regulator of Hsp70 proteins / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
BAG family molecular chaperone regulator 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsHuang, H. / Yu, C.
Citation
Journal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: The NMR solution structure of the ubiquitin homology domain of Bcl-2-associated athanogene 1 (BAG-1-UBH) from Mus musculus.
Authors: Huang, H.W. / Yu, C.
#1: Journal: To be Published
Title: 1H, 15N and 13 C resonance assignments of ubiquitin homology of mouse BAG-1
Authors: Huang, H. / Yu, C.
History
DepositionAug 5, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 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: BAG family molecular chaperone regulator 1


Theoretical massNumber of molelcules
Total (without water)10,7991
Polymers10,7991
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)18 / 200structures with the lowest energy
RepresentativeModel #1minimized average structure

-
Components

#1: Protein BAG family molecular chaperone regulator 1 / BAG-1 / Bcl-2-associated athanogene 1


Mass: 10799.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bag1 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60739

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D C(CO)NH
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HN(CO)CA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY

-
Sample preparation

DetailsContents: 1.0 mM [U-100% 13C; U-100% 15N] ubiquitin homology domain of mouse BAG, 20 mM sodium phosphate, 100 mM sodium chloride, 5 mM DTT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMubiquitin homology domain of mouse BAG-1-1[U-100% 13C; U-100% 15N]1
20 mMsodium phosphate-21
100 mMsodium chloride-31
5 mMDTT-41
Sample conditionsIonic strength: 0.1 / pH: 6 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Varian VNMR / Manufacturer: Varian / Model: VNMR / Field strength: 700 MHz

-
Processing

NMR softwareName: CNS / Developer: Brunger A. T. et.al. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 18

+
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