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- PDB-1gc7: CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1gc7
TitleCRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN
ComponentsRADIXIN
KeywordsCELL ADHESION / 3 subdomains / CYTOSKELETON
Function / homology
Function and homology information


negative regulation of homotypic cell-cell adhesion / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / microvillus assembly / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / cell tip ...negative regulation of homotypic cell-cell adhesion / regulation of actin filament bundle assembly / regulation of organelle assembly / regulation of ruffle assembly / establishment of protein localization to plasma membrane / microvillus assembly / negative regulation of adherens junction organization / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / cell tip / Recycling pathway of L1 / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / stereocilium / apical protein localization / barbed-end actin filament capping / negative regulation of cell size / establishment of endothelial barrier / cellular response to thyroid hormone stimulus / protein kinase A binding / regulation of cell size / cortical actin cytoskeleton / cleavage furrow / microvillus / positive regulation of G1/S transition of mitotic cell cycle / protein kinase A signaling / ruffle / T-tubule / cell adhesion molecule binding / filopodium / cell periphery / protein localization to plasma membrane / adherens junction / establishment of protein localization / positive regulation of protein catabolic process / apical part of cell / lamellipodium / myelin sheath / actin binding / midbody / ATPase binding / regulation of cell shape / positive regulation of cell migration / apical plasma membrane / protein domain specific binding / positive regulation of gene expression / plasma membrane / cytosol
Similarity search - Function
Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein ...Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin, alpha-helical domain / Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin family C terminal / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like / Acyl-CoA Binding Protein / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM domain signature 1. / FERM conserved site / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsHamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
Citation
Journal: EMBO J. / Year: 2000
Title: Structural basis of the membrane-targeting and unmasking mechanisms of the radixin FERM domain.
Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Hakoshima, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallographic characterization of the membrane-binding domain of radixin
Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
History
DepositionJul 21, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RADIXIN


Theoretical massNumber of molelcules
Total (without water)35,2791
Polymers35,2791
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.330, 96.330, 133.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RADIXIN /


Mass: 35278.723 Da / Num. of mol.: 1 / Fragment: FERM DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PGEX4T-3 / Production host: Escherichia coli (E. coli) / References: UniProt: P26043

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 4.37 Å3/Da / Density % sol: 71.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMMES-Na1reservoir
32 %PEG60001reservoir
4150 mM1reservoirNaCl
50.5 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Mar 2, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 161048 / Num. obs: 23751 / % possible obs: 99.8 % / Biso Wilson estimate: 64.2 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.8
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.393 / % possible all: 99.9
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.8→30 Å / σ(F): 2 / Stereochemistry target values: protein.param
RfactorNum. reflectionSelection details
Rfree0.255 765 RANDOM
Rwork0.215 --
all-16033 -
obs-15929 -
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 0 2482
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.442
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.863

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