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- PDB-2lwp: The NMR solution structure of the the ubiquitin homology domain o... -

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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 / positive regulation of Schwann cell differentiation / protein localization to mitochondrion / negative regulation of motor neuron apoptotic process / negative regulation of protein phosphorylation / neuron differentiation / protein-folding chaperone binding / protein stabilization ...Regulation of HSF1-mediated heat shock response / adenyl-nucleotide exchange factor activity / positive regulation of smooth muscle cell apoptotic process / positive regulation of Schwann cell differentiation / protein localization to mitochondrion / negative regulation of motor neuron apoptotic process / negative regulation of protein phosphorylation / neuron differentiation / protein-folding chaperone binding / protein stabilization / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
BAG domain superfamily / Molecular chaperone regulator BAG / 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 ...BAG domain superfamily / Molecular chaperone regulator BAG / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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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

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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: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

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

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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

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