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- PDB-7m0g: Magic Angle Spinning NMR Structure of Human Cofilin-2 Assembled o... -

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Basic information

Entry
Database: PDB / ID: 7m0g
TitleMagic Angle Spinning NMR Structure of Human Cofilin-2 Assembled on Actin Filaments
ComponentsCofilin-2
KeywordsCONTRACTILE PROTEIN / actin filament binding / actin filament severing / cytoskeletal assembly
Function / homology
Function and homology information


actin filament fragmentation / positive regulation of actin filament depolymerization / actin filament severing / actin filament depolymerization / I band / muscle cell cellular homeostasis / sarcomere organization / skeletal muscle tissue development / cell motility / nuclear matrix ...actin filament fragmentation / positive regulation of actin filament depolymerization / actin filament severing / actin filament depolymerization / I band / muscle cell cellular homeostasis / sarcomere organization / skeletal muscle tissue development / cell motility / nuclear matrix / Z disc / actin filament binding / actin cytoskeleton / extracellular space / extracellular exosome / 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 / ADF-H/Gelsolin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / simulated annealing
AuthorsKraus, J. / Polenova, T. / Perilla, J.P. / Xu, C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1247394 United States
National Science Foundation (NSF, United States)CHE0959496 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110758 United States
CitationJournal: Nat Commun / Year: 2022
Title: Magic angle spinning NMR structure of human cofilin-2 assembled on actin filaments reveals isoform-specific conformation and binding mode.
Authors: Kraus, J. / Russell, R.W. / Kudryashova, E. / Xu, C. / Katyal, N. / Perilla, J.R. / Kudryashov, D.S. / Polenova, T.
History
DepositionMar 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
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-2


Theoretical massNumber of molelcules
Total (without water)18,7661
Polymers18,7661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, Confirmed by negative-stain TEM and co-sedimentation assay
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 250structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cofilin-2 / Cofilin / muscle isoform


Mass: 18765.627 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y281

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic1Exp1 CORD50ms
121isotropic1Exp2 CORD200ms
132isotropic1Exp3 CORD50ms
142isotropic1Exp4 CORD200ms
152isotropic1Exp5 CORD500ms
163isotropic1Exp6 CORD50ms
173isotropic1Exp7 CORD200ms
183isotropic1Exp8 CORD500ms
193isotropic1Exp9 PAINCP
1101isotropic1Exp10 NCACX2d
1111isotropic1Exp11 NCACX3d
1121isotropic1Exp12 NCOCX2d
1131isotropic1Exp13 NCOCX3d

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solid120.8 % w/w [U-13C; U-15N] human cofilin-2, 79.2 % w/w NA-actin F-actin, solidUniformly labeled human cofilin-2 in complex with natural abundance actin filaments obtained using rabbit skeletal muscle actin[U-13C; U-15N]-cofilin2solid
solid220.8 % w/w [1,6-13C]-glucose, U-15N human cofilin-2, 79.2 % w/w NA-actin F-actin, solidSelectively labeled human cofilin-2 in complex with natural abundance actin filaments obtained using rabbit skeletal muscle actin[1,6-13C]-glucose, U-15N-cofilin2solid
solid320.8 % w/w [2-13C]-glucose, U-15N human cofilin-2, 79.2 % w/w NA-actin F-actin, solidSelectively labeled human cofilin-2 in complex with natural abundance actin filaments obtained using rabbit skeletal muscle actin[2-13C]-glucose, U-15N-cofilin2solid
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20.8 % w/whuman cofilin-2[U-13C; U-15N]1
79.2 % w/wF-actinNA-actin1
20.8 % w/whuman cofilin-2[1,6-13C]-glucose, U-15N2
79.2 % w/wF-actinNA-actin2
20.8 % w/whuman cofilin-2[2-13C]-glucose, U-15N3
79.2 % w/wF-actinNA-actin3
Sample conditionsIonic strength: 50 mM / Label: cofilin condition / pH: 6.6 / Pressure: 1 atm / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 850 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Rowland NMR Toolkit (RNMRTK)Hoch and Sternprocessing
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TALOS-NCornilescu, Delaglio and Baxstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 250 / Conformers submitted total number: 10

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