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- PDB-2krh: Structure of the C-terminal actin binding domain of ABRA -

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Basic information

Entry
Database: PDB / ID: 2krh
TitleStructure of the C-terminal actin binding domain of ABRA
ComponentsActin-binding Rho-activating protein
KeywordsACTIN-BINDING PROTEIN / muscle / actin binding / stress response / cardiac / Actin-binding / Cytoskeleton
Function / homology
Function and homology information


positive regulation of Rho protein signal transduction / myofibril / sarcomere / protein import into nucleus / actin cytoskeleton / actin binding / actin cytoskeleton organization / transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Actin-binding Rho-activating protein / Costar domain / Costars domain / Costars domain superfamily / Costars / Costars / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Actin-binding Rho-activating protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsSolution state NMR structure of the second actin binding domain of ms1/STARS/ABRA.
AuthorsFogl, C.L.F. / Pfuhl, M.
CitationJournal: To be Published
Title: Structure of the C-terminal actin binding domain of ABRA
Authors: Fogl, C.L.F. / Pfuhl, M.
History
DepositionDec 18, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Actin-binding Rho-activating protein


Theoretical massNumber of molelcules
Total (without water)10,0451
Polymers10,0451
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Actin-binding Rho-activating protein / ms1 / STARS / ABRA / Striated muscle activator of Rho-dependent signaling


Mass: 10044.783 Da / Num. of mol.: 1 / Fragment: C-terminal actin binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Abra, Ms1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): BL21 STAR (Invitrogen) / References: UniProt: Q8K4K7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Solution state NMR structure of the second actin binding domain of ms1/STARS/ABRA.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 1H-13C NOESY
1223D 1H-15N NOESY
1332D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.350mM [U-95% 13C; U-95% 15N] ABD2, 50mM sodium chloride, 20mM sodium phosphate, 2mM DTT, 0.02% sodium azide, 95% H2O/5% D2O95% H2O/5% D2O
20.300mM [U-95% 15N] ABD2, 50mM sodium chloride, 20mM sodium phosphate, 2mM DTT, 0.02% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
30.250mM ABD2, 50mM sodium chloride, 20mM sodium phosphate, 2mM DTT, 0.02% sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
350 uMABD2[U-95% 13C; U-95% 15N]1
50 mMsodium chloride1
20 mMsodium phosphate1
2 mMDTT1
0.02 %sodium azide1
300 uMABD2[U-95% 15N]2
50 mMsodium chloride2
20 mMsodium phosphate2
2 mMDTT2
0.02 %sodium azide2
250 uMABD23
50 mMsodium chloride3
20 mMsodium phosphate3
2 mMDTT3
0.02 %sodium azide3
Sample conditionsIonic strength: 0.15 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE6002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinprocessing
Analysis1CCPNchemical shift assignment
Analysis1CCPNpeak picking
Analysis1CCPNchemical shift calculation
Analysis1CCPNdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
TALOS2006Cornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3648 / NOE intraresidue total count: 813 / NOE long range total count: 566 / NOE medium range total count: 390 / NOE sequential total count: 1879 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 84 / Protein psi angle constraints total count: 84
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.3669 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.02 Å / Maximum torsion angle constraint violation: 0.4822 ° / Maximum upper distance constraint violation: 0.14 Å / Representative conformer: 1

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