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- PDB-2mv2: Solution structure of Twinstar from Drosophila melanogastor -

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Basic information

Entry
Database: PDB / ID: 2mv2
TitleSolution structure of Twinstar from Drosophila melanogastor
ComponentsCofilin/actin-depolymerizing factor homolog
KeywordsACTIN BINDING PROTEIN / ADF-h fold
Function / homology
Function and homology information


establishment of imaginal disc-derived wing hair orientation / establishment of ommatidial planar polarity / imaginal disc-derived leg segmentation / meiotic cytokinesis / compound eye morphogenesis / mushroom body development / rhabdomere development / actin filament fragmentation / actomyosin contractile ring assembly / border follicle cell migration ...establishment of imaginal disc-derived wing hair orientation / establishment of ommatidial planar polarity / imaginal disc-derived leg segmentation / meiotic cytokinesis / compound eye morphogenesis / mushroom body development / rhabdomere development / actin filament fragmentation / actomyosin contractile ring assembly / border follicle cell migration / compound eye development / centrosome separation / establishment of planar polarity / epithelial structure maintenance / actin filament severing / actin filament depolymerization / regulation of lamellipodium assembly / lamellipodium assembly / female gonad development / mitotic cytokinesis / actin filament polymerization / axonogenesis / actin filament organization / positive regulation of protein secretion / nuclear matrix / actin filament binding / actin cytoskeleton / actin binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / Severin / Severin / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cofilin/actin-depolymerizing factor homolog
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsShukla, V.K. / Maheshwari, D. / Kumar, D. / Arora, A.
CitationJournal: To be Published
Title: Solution structure and dynamics of Twinstar from Drosophila melanogastor
Authors: Shukla, V.K. / Maheshwari, D. / Jain, A. / Tripathi, S. / Kumar, D. / Arora, A.
History
DepositionSep 20, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_spectrometer.model
Revision 1.3May 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: Cofilin/actin-depolymerizing factor homolog


Theoretical massNumber of molelcules
Total (without water)17,1811
Polymers17,1811
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)10 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Cofilin/actin-depolymerizing factor homolog / Protein D61 / Protein twinstar


Mass: 17180.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: tsr, Cadf, CG4254 / Production host: Escherichia coli (E. coli) / References: UniProt: P45594

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1223D CBCA(CO)NH
132HNCANH
1423D HNCA
1523D HNCO
1623D H(CCO)NH
1723D C(CO)NH
1833D (H)CCH-TOCSY
1922D 1H-13C HSQC aliphatic
11032D 1H-13C HSQC aromatic
11133D 1H-13C NOESY aliphatic
11233D 1H-13C NOESY aromatic
11313D 1H-15N NOESY
1143CBHD
1153CBHE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1 % w/v [U-99% 15N] ammonium sulfate, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM DTT, 0.1 % w/v sodium azide, 93% H2O/7% D2O93% H2O/7% D2O
20.1 % w/v [U-99% 15N] ammonium sulfate, 0.2 % w/v [U-100% 13C] Glucose, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % w/v sodium azide, 1 mM DTT, 93% H2O/7% D2O93% H2O/7% D2O
30.1 % w/v [U-99% 15N] ammonium sulfate, 0.2 % w/v [U-100% 13C] Glucose, 20 mM sodium phosphate, 50 mM sodium chloride, 0.1 % w/v sodium azide, 1 mM DTT, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.1 %ammonium sulfate-1[U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
0.1 %sodium azide-51
0.1 %ammonium sulfate-6[U-99% 15N]2
0.2 %Glucose-7[U-100% 13C]2
20 mMsodium phosphate-82
50 mMsodium chloride-92
0.1 %sodium azide-102
1 mMDTT-112
0.1 %ammonium sulfate-12[U-99% 15N]3
0.2 %Glucose-13[U-100% 13C]3
20 mMsodium phosphate-143
50 mMsodium chloride-153
0.1 %sodium azide-163
1 mMDTT-173
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 25 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CARAKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
TopSpinBruker Biospinprocessing
PSVSBhattacharya and Montelionestructure validation
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 10

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