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- PDB-1gc6: CRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN COMPLEXED WITH INOSI... -

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Basic information

Entry
Database: PDB / ID: 1gc6
TitleCRYSTAL STRUCTURE OF THE RADIXIN FERM DOMAIN COMPLEXED WITH INOSITOL-(1,4,5)-TRIPHOSPHATE
ComponentsRADIXIN
KeywordsCELL ADHESION / CYTOSKELETON
Function / homology
Function and homology information


stereocilium base / regulation of organelle assembly / establishment of protein localization to plasma membrane / microvillus assembly / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / Recycling pathway of L1 / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome ...stereocilium base / regulation of organelle assembly / establishment of protein localization to plasma membrane / microvillus assembly / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / Recycling pathway of L1 / cell tip / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / apical protein localization / stereocilium / barbed-end actin filament capping / cellular response to thyroid hormone stimulus / protein kinase A binding / cortical actin cytoskeleton / cleavage furrow / microvillus / positive regulation of G1/S transition of mitotic cell cycle / cell adhesion molecule binding / ruffle / protein kinase A signaling / T-tubule / filopodium / adherens junction / establishment of protein localization / lamellipodium / apical part of cell / myelin sheath / actin binding / regulation of cell shape / midbody / protein domain specific binding / 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
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / Radixin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RADIXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6992
Polymers35,2791
Non-polymers4201
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.800, 96.800, 132.750
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
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3

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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: 4.41 Å3/Da / Density % sol: 72.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 6000, MES, INOSITOL-(1,4,5)-TRIPHOSPHATE, 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: ROTATING ANODE / Type: RIGAKU FR-C / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 21, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 88728 / Num. obs: 14511 / % possible obs: 99.5 % / Biso Wilson estimate: 63.6 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.9
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.485 / % possible all: 98.8
Reflection shell
*PLUS
% possible obs: 98.8 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→30 Å / σ(F): 2 / Stereochemistry target values: protein.para
RfactorNum. reflectionSelection details
Rfree0.283 724 RANDOM
Rwork0.229 --
all-14582 -
obs-14481 -
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 24 0 2506
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.478
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.205

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