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- PDB-2ems: Crystal Structure Analysis of the radixin FERM domain complexed w... -

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Basic information

Entry
Database: PDB / ID: 2ems
TitleCrystal Structure Analysis of the radixin FERM domain complexed with adhesion molecule CD43
Components
  • Leukosialin
  • Radixin
KeywordsCELL ADHESION / Protein-peptide complex
Function / homology
Function and homology information


response to protozoan / negative regulation of type IV hypersensitivity / stereocilium base / Basigin interactions / regulation of organelle assembly / establishment of protein localization to plasma membrane / regulation of T cell migration / microvillus assembly / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction ...response to protozoan / negative regulation of type IV hypersensitivity / stereocilium base / Basigin interactions / regulation of organelle assembly / establishment of protein localization to plasma membrane / regulation of T cell migration / microvillus assembly / positive regulation of early endosome to late endosome transport / regulation of Rap protein signal transduction / T-helper 1 cell lineage commitment / Recycling pathway of L1 / cell tip / uropod / Cell surface interactions at the vascular wall / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / negative regulation of T cell activation / negative thymic T cell selection / regulation of defense response to virus / leukocyte tethering or rolling / stereocilium / apical protein localization / barbed-end actin filament capping / negative regulation of cell adhesion / cellular response to thyroid hormone stimulus / protein kinase A binding / cortical actin cytoskeleton / cleavage furrow / microvillus / regulation of immune response / basement membrane / positive regulation of T cell migration / positive regulation of G1/S transition of mitotic cell cycle / negative regulation of T cell proliferation / cell adhesion molecule binding / positive regulation of T cell proliferation / T cell proliferation / heat shock protein binding / ruffle / T-tubule / T cell costimulation / protein kinase A signaling / Hsp70 protein binding / filopodium / apoptotic signaling pathway / adherens junction / establishment of protein localization / PML body / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / apical part of cell / lamellipodium / myelin sheath / regulation of cell shape / actin binding / midbody / cell surface receptor signaling pathway / defense response to bacterium / positive regulation of protein phosphorylation / protein domain specific binding / external side of plasma membrane / cell surface / extracellular space / plasma membrane / cytosol
Similarity search - Function
Leukosialin / 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 / Acyl-CoA Binding Protein - #10 / Ezrin/radixin/moesin-like ...Leukosialin / 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 / 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) / PH-domain like / FERM central domain / 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
Leukosialin / Radixin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTakai, Y. / Kitano, K. / Terawaki, S. / Maesaki, R. / Hakoshima, T.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural basis of the cytoplasmic tail of adhesion molecule CD43 and its binding to ERM proteins
Authors: Takai, Y. / Kitano, K. / Terawaki, S. / Maesaki, R. / Hakoshima, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tails of adhesion molecules CD43 and PSGL-1
Authors: Takai, Y. / Kitano, K. / Terawaki, S. / Maesaki, R. / Hakoshima, T.
History
DepositionMar 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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: Leukosialin


Theoretical massNumber of molelcules
Total (without water)40,2032
Polymers40,2032
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-6.7 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.699, 68.699, 201.325
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Radixin / ESP10


Mass: 37955.652 Da / Num. of mol.: 1 / Fragment: N-terminal 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) / References: UniProt: P26043
#2: Protein/peptide Leukosialin / Leukocyte sialoglycoprotein / Sialophorin / Ly- 48 / B cell differentiation antigen LP-3 / CD43 antigen


Mass: 2247.590 Da / Num. of mol.: 1
Fragment: CD43 cytoplasmic peptide, 20 N-terminal residues of the cytoplasmic tail
Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / References: UniProt: P15702

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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: 2.95 Å3/Da / Density % sol: 58.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% PEG 4000, 10% iso-propanol, 0.1M Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MAC Science DIP-2040B / Detector: IMAGE PLATE / Date: Dec 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 11007 / % possible obs: 96.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 87.6 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 7.7
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.377 / % possible all: 76.4

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1J19

1j19


Resolution: 2.9→48.01 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2101909.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1082 10.3 %RANDOM
Rwork0.236 ---
obs0.236 10477 92.2 %-
all-11007 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.1396 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 86.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.98 Å20 Å20 Å2
2--5.98 Å20 Å2
3----11.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.65 Å
Refinement stepCycle: LAST / Resolution: 2.9→48.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 0 0 2712
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 146 10.2 %
Rwork0.347 1281 -
obs--77.9 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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