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

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Basic information

Entry
Database: PDB / ID: 2emt
TitleCrystal Structure Analysis of the radixin FERM domain complexed with adhesion molecule PSGL-1
Components
  • P-selectin glycoprotein ligand 1
  • Radixin
KeywordsCELL ADHESION / Protein-peptide complex
Function / homology
Function and homology information


leukocyte adhesive activation / stereocilium base / microvillus assembly / Recycling pathway of L1 / Cell surface interactions at the vascular wall / regulation of postsynaptic neurotransmitter receptor diffusion trapping / leukocyte tethering or rolling / stereocilium / actin filament capping / apical protein localization ...leukocyte adhesive activation / stereocilium base / microvillus assembly / Recycling pathway of L1 / Cell surface interactions at the vascular wall / regulation of postsynaptic neurotransmitter receptor diffusion trapping / leukocyte tethering or rolling / stereocilium / actin filament capping / apical protein localization / cellular response to thyroid hormone stimulus / cortical actin cytoskeleton / cleavage furrow / microvillus / positive regulation of G1/S transition of mitotic cell cycle / ruffle / filopodium / establishment of protein localization / apical part of cell / lamellipodium / myelin sheath / actin binding / protein domain specific binding / plasma membrane / cytosol
Similarity search - Function
P-selectin glycoprotein ligand 1 / 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 ...P-selectin glycoprotein ligand 1 / 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) / 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
Radixin / P-selectin glycoprotein ligand 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTakai, Y. / Kitano, K. / Terawaki, S. / Maesaki, R. / Hakoshima, T.
Citation
Journal: Genes Cells / Year: 2007
Title: Structural basis of PSGL-1 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 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 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: Radixin
C: P-selectin glycoprotein ligand 1
D: P-selectin glycoprotein ligand 1
E: P-selectin glycoprotein ligand 1


Theoretical massNumber of molelcules
Total (without water)82,6335
Polymers82,6335
Non-polymers00
Water00
1
A: Radixin
C: P-selectin glycoprotein ligand 1
E: P-selectin glycoprotein ligand 1


Theoretical massNumber of molelcules
Total (without water)42,4373
Polymers42,4373
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11.2 kcal/mol
Surface area19200 Å2
MethodPISA
2
B: Radixin
D: P-selectin glycoprotein ligand 1


Theoretical massNumber of molelcules
Total (without water)40,1962
Polymers40,1962
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-7.2 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.740, 85.730, 117.751
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: 37955.652 Da / Num. of mol.: 2 / 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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P26043
#2: Protein/peptide P-selectin glycoprotein ligand 1 / PSGL-1 / Selectin P ligand


Mass: 2240.564 Da / Num. of mol.: 3
Fragment: PSGL-1 cytoplasmic peptide, 18 N-terminal residues of the cytoplasmic tail
Source method: obtained synthetically / Details: This sequence occurs naturally in mouse. / References: UniProt: Q62170

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 8% PEG 8000, 0.1M Tris-HCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 8, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20429 / % possible obs: 98.4 % / Redundancy: 1.9 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 9.2
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.117 / % possible all: 92.3

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Processing

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

1j19


Resolution: 2.8→48.53 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1541734.41 / 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
Rfree0.294 1907 9.9 %RANDOM
Rwork0.235 ---
obs0.235 19356 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.4079 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.84 Å20 Å20 Å2
2--16.73 Å20 Å2
3----6.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5565 0 0 0 5565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.91
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 283 9.4 %
Rwork0.347 2725 -
obs--88.7 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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