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- PDB-1q8x: NMR structure of human cofilin -

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Basic information

Entry
Database: PDB / ID: 1q8x
TitleNMR structure of human cofilin
ComponentsCofilin, non-muscle isoform
KeywordsSTRUCTURAL PROTEIN / ADF/cofilin / chemical shift perturbation / actin cytoskeleton / G-actin binding
Function / homology
Function and homology information


actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / lamellipodium membrane ...actin filament fragmentation / positive regulation of embryonic development / establishment of spindle localization / actin filament severing / regulation of dendritic spine morphogenesis / positive regulation by host of viral process / actin filament depolymerization / RHO GTPases Activate ROCKs / regulation of cell morphogenesis / lamellipodium membrane / mitotic cytokinesis / Sema3A PAK dependent Axon repulsion / Rho protein signal transduction / cytoskeleton organization / EPHB-mediated forward signaling / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to virus / Regulation of actin dynamics for phagocytic cup formation / ruffle membrane / nuclear matrix / actin filament binding / actin cytoskeleton / Platelet degranulation / lamellipodium / growth cone / actin cytoskeleton organization / vesicle / focal adhesion / negative regulation of apoptotic process / extracellular space / extracellular exosome / membrane / nucleus / 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
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
AuthorsPope, B.J. / Zierler-Gould, K.M. / Kuhne, R. / Weeds, A.G. / Ball, L.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The solution structure of human cofilin: rationalizing actin binding and pH sensitivity
Authors: Pope, B.J. / Zierler-Gould, K.M. / Kuhne, R. / Weeds, A.G. / Ball, L.J.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cofilin, non-muscle isoform


Theoretical massNumber of molelcules
Total (without water)18,5331
Polymers18,5331
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cofilin, non-muscle isoform / 18 kDa phosphoprotein / P18


Mass: 18532.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1 OR CFL / Plasmid: pMW172 / Production host: Escherichia coli (E. coli) / Strain (production host): BL27(DE3) / References: UniProt: P23528

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
2223D 15N-separated NOESY
2322D NOESY
2422D TOCSY
252DQF-COSY
262HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM cofilin U-15N,13C; 10mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
21 mM cofilin U-15N, 10mM phosphate buffer; 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1161 atm300 K
2161 atm300 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR1.3Bruker AGcollection
XwinNMR1.3Bruker AGprocessing
Azara2.1Boucher, W.processing
ANSIG3.3Kraulis, P.J.data analysis
CYANA1.1Guenthert, P.structure solution
CYANA1.1Guenthert, P.refinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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