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- PDB-4bex: Structure of human Cofilin1 -

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Basic information

Entry
Database: PDB / ID: 4bex
TitleStructure of human Cofilin1
ComponentsCOFILIN-1
KeywordsSTRUCTURAL PROTEIN / ACTIN-BINDING / CYTOSKELETON
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 / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / mitotic cytokinesis / 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 / nuclear matrix / ruffle membrane / 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 / cytoplasm / cytosol
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKlejnot, M. / Gabrielsen, M. / Cameron, J. / Mleczak, A. / Talapatra, S.K. / Kozielski, F. / Pannifer, A. / Olson, M.F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Analysis of the Human Cofilin1 Structure Reveals Conformational Changes Required for Actin-Binding
Authors: Klejnot, M. / Gabrielsen, M. / Cameron, J. / Mleczak, A. / Talapatra, S.K. / Kozielski, F. / Pannifer, A. / Olson, M.F.
History
DepositionMar 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references / Structure summary
Revision 1.2Sep 18, 2013Group: Structure summary
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: COFILIN-1


Theoretical massNumber of molelcules
Total (without water)19,7131
Polymers19,7131
Non-polymers00
Water28816
1
1: COFILIN-1

1: COFILIN-1


Theoretical massNumber of molelcules
Total (without water)39,4252
Polymers39,4252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area1160 Å2
ΔGint-10.4 kcal/mol
Surface area17210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.940, 85.940, 85.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
111-139-

CYS

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Components

#1: Protein COFILIN-1 / 18 KDA PHOSPHOPROTEIN / P18 / COFILIN / NON-MUSCLE ISOFORM


Mass: 19712.748 Da / Num. of mol.: 1 / Fragment: COFILIN-LIKE FOLD, RESIDUES 1-166 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P23528
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.92 Å3/Da / Density % sol: 75.04 % / Description: NONE
Crystal growpH: 7
Details: 2.4 M SODIUM MALONATE PH 7.0 THE CRYSTALS WERE AIR-DRIED BEFORE FREEZING TO DEHYDRATE.

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2011 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→74.4 Å / Num. obs: 9292 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 84.06 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COF

1cof


Resolution: 2.8→28.13 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 26.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 442 4.8 %
Rwork0.2065 --
obs0.2079 9292 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.75 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 0 16 1310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071314
X-RAY DIFFRACTIONf_angle_d1.0731760
X-RAY DIFFRACTIONf_dihedral_angle_d16.638509
X-RAY DIFFRACTIONf_chiral_restr0.068201
X-RAY DIFFRACTIONf_plane_restr0.005221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8002-3.2050.31361480.25952893X-RAY DIFFRACTION100
3.205-4.0360.23471440.21622929X-RAY DIFFRACTION100
4.036-28.13180.22091500.19283028X-RAY DIFFRACTION100

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