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- PDB-2zpy: Crystal structure of the mouse radxin FERM domain complexed with ... -

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Basic information

Entry
Database: PDB / ID: 2zpy
TitleCrystal structure of the mouse radxin FERM domain complexed with the mouse CD44 cytoplasmic peptide
Components
  • CD44 antigen
  • Radixin
KeywordsCELL ADHESION / FERM domain / CD44 / Actin capping / Actin-binding / Cell membrane / Cytoplasm / Cytoskeleton / Membrane / Phosphoprotein / Structural protein / Alternative splicing / Glycoprotein / Proteoglycan / Pyrrolidone carboxylic acid / Receptor / Sulfation / Transmembrane
Function / homology
Function and homology information


stereocilium base / Hyaluronan uptake and degradation / microvillus assembly / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Recycling pathway of L1 / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions ...stereocilium base / Hyaluronan uptake and degradation / microvillus assembly / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Recycling pathway of L1 / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / positive regulation of adaptive immune response / wound healing involved in inflammatory response / hyaluronan catabolic process / regulation of postsynaptic neurotransmitter receptor diffusion trapping / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / channel regulator activity / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / actin filament capping / stereocilium / apical protein localization / cellular response to thyroid hormone stimulus / wound healing, spreading of cells / cargo receptor activity / branching involved in ureteric bud morphogenesis / cortical actin cytoskeleton / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / cleavage furrow / microvillus / lamellipodium membrane / positive regulation of G1/S transition of mitotic cell cycle / ruffle / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / filopodium / establishment of protein localization / cytokine-mediated signaling pathway / negative regulation of inflammatory response / Wnt signaling pathway / apical part of cell / lamellipodium / myelin sheath / actin binding / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / protein domain specific binding / membrane raft / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular region / plasma membrane / cytosol
Similarity search - Function
Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / CD44 antigen / CD44 antigen-like / Link domain signature. ...Moesin tail domain superfamily / Ezrin/radixin/moesin / Ezrin/radixin/moesin, C-terminal / ERM family, FERM domain C-lobe / Ezrin/radixin/moesin, alpha-helical domain / Ezrin/radixin/moesin family C terminal / Ezrin/radixin/moesin, alpha-helical domain / CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / 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) / C-type lectin-like/link domain superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / PH-domain like / C-type lectin fold / 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
CD44 antigen / Radixin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMori, T. / Kitano, K. / Terawaki, S. / Maesaki, R. / Fukami, Y. / Hakoshima, T.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Structural basis for CD44 recognition by ERM proteins
Authors: Mori, T. / Kitano, K. / Terawaki, S. / Maesaki, R. / Fukami, Y. / Hakoshima, T.
History
DepositionJul 31, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Radixin
B: CD44 antigen


Theoretical massNumber of molelcules
Total (without water)39,1122
Polymers39,1122
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-7 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.700, 66.182, 86.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Radixin / ESP10


Mass: 36934.598 Da / Num. of mol.: 1 / Fragment: FERM domain (residues 1-310)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rdx / Plasmid: pET49b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P26043
#2: Protein/peptide CD44 antigen


Mass: 2177.579 Da / Num. of mol.: 1 / Fragment: residues 293-312 / Source method: obtained synthetically / Details: peptide synthesis / References: UniProt: P15379
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.29 Å3/Da / Density % sol: 46.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.6
Details: 0.1M Tris, 0.2M Potassium thiocyanate, 15% PEG 3350 , pH 8.6, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 17, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 21492 / % possible obs: 100 %
Reflection shellResolution: 2.1→2.17 Å / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GC7

1gc7


Resolution: 2.1→20 Å
RfactorNum. reflectionSelection details
Rfree0.256 -RANDOM
Rwork0.231 --
obs-21492 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 0 171 2714

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