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- PDB-2d2q: Crystal structure of the dimerized radixin FERM domain -

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Basic information

Entry
Database: PDB / ID: 2d2q
TitleCrystal structure of the dimerized radixin FERM domain
ComponentsRadixin
KeywordsCELL ADHESION / Homo dimer / Masking
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 / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKitano, K. / Yusa, F. / Hakoshima, T.
CitationJournal: ACTA CRYSTALLOGR.,SECT.F / Year: 2006
Title: Structure of dimerized radixin FERM domain suggests a novel masking motif in C-terminal residues 295-304
Authors: Kitano, K. / Yusa, F. / Hakoshima, T.
History
DepositionSep 15, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: 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
B: Radixin


Theoretical massNumber of molelcules
Total (without water)73,5612
Polymers73,5612
Non-polymers00
Water0
1
A: Radixin


Theoretical massNumber of molelcules
Total (without water)36,7801
Polymers36,7801
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Radixin


Theoretical massNumber of molelcules
Total (without water)36,7801
Polymers36,7801
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.218, 70.218, 110.810
Angle α, β, γ (deg.)90.00, 98.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Radixin / / ESP10


Mass: 36780.430 Da / Num. of mol.: 2 / Fragment: FERM domain (residues 1-310)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX4T-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P26043

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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: 2.98 Å3/Da / Density % sol: 58.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: PEG 3350, HEPES-Na, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 19703 / Num. obs: 19703 / % possible obs: 96.4 %
Reflection shellResolution: 2.8→2.9 Å / % possible all: 76.9

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.269 899 RANDOM
Rwork0.222 --
all-19703 -
obs-19703 -
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5016 0 0 0 5016

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