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- PDB-1j19: Crystal structure of the radxin FERM domain complexed with the IC... -

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Basic information

Entry
Database: PDB / ID: 1j19
TitleCrystal structure of the radxin FERM domain complexed with the ICAM-2 cytoplasmic peptide
Components
  • 16-mer peptide from Intercellular adhesion molecule-2
  • radixin
KeywordsCELL ADHESION / protein-peptide complex
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 / uropod / cell tip / Integrin cell surface interactions ...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 / uropod / cell tip / Integrin cell surface interactions / regulation of postsynaptic neurotransmitter receptor diffusion trapping / positive regulation of protein localization to early endosome / CD209 (DC-SIGN) signaling / stereocilium / apical protein localization / barbed-end actin filament capping / cellular response to thyroid hormone stimulus / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / T-tubule / protein kinase A signaling / filopodium / cell periphery / adherens junction / establishment of protein localization / cell-cell adhesion / integrin binding / apical part of cell / lamellipodium / myelin sheath / regulation of cell shape / actin binding / midbody / cell adhesion / protein domain specific binding / plasma membrane / cytosol
Similarity search - Function
Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / 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 ...Intercellular adhesion molecule, N-terminal / Intercellular adhesion molecule (ICAM), N-terminal domain / Intercellular adhesion molecule/vascular cell adhesion molecule, N-terminal / : / 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 / Immunoglobulin-like domain superfamily / Roll / Immunoglobulin-like fold / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Radixin / Intercellular adhesion molecule 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHamada, K. / Shimizu, T. / Yonemura, S. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
Citation
Journal: EMBO J. / Year: 2003
Title: Structural basis of adhesion-molecule recognition by ERM proteins revealed by the crystal structure of the radixin-ICAM-2 complex
Authors: Hamada, K. / Shimizu, T. / Yonemura, S. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallographic characterization of the radixin FERM domain bound to the cytoplasmic tail of the adhesion protein ICAM-2
Authors: Hamada, K. / Shimizu, T. / Matsui, T. / Tsukita, S. / Tsukita, S. / Hakoshima, T.
History
DepositionDec 2, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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: 16-mer peptide from Intercellular adhesion molecule-2


Theoretical massNumber of molelcules
Total (without water)39,3052
Polymers39,3052
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-9 kcal/mol
Surface area17860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.440, 100.440, 99.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein radixin


Mass: 37368.008 Da / Num. of mol.: 1 / Fragment: N-terminal domain, FERM domain
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 16-mer peptide from Intercellular adhesion molecule-2 / ICAM-2 cytoplasmic peptide / ICAM-2 cytoplasmic tail


Mass: 1937.281 Da / Num. of mol.: 1
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: P35330
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG6000, MES, NaCl, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.27 mMprotein/peptide solution11
250 mMMES/Na12pH6.0
32 %PEG600012
4130 mM12NaCl
50.4 mMdithiothreitol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→44.7 Å / Num. all: 599708 / Num. obs: 23153 / % possible obs: 100 % / Biso Wilson estimate: 41.7 Å2
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.137 / Mean I/σ(I) obs: 5.2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.4 Å / % possible obs: 100 % / Num. measured all: 599708 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GC7

1gc7


Resolution: 2.4→14.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1411875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2269 9.9 %RANDOM
Rwork0.228 ---
obs0.228 23002 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.0264 Å2 / ksol: 0.328436 e/Å3
Displacement parametersBiso mean: 52.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.22 Å2-1.81 Å20 Å2
2---6.05 Å20 Å2
3---11.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.4→14.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 0 232 2966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.812
X-RAY DIFFRACTIONc_scbond_it10.492
X-RAY DIFFRACTIONc_scangle_it9.922.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 353 9.3 %
Rwork0.348 3423 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAM
Refinement
*PLUS
Lowest resolution: 15 Å / % reflection Rfree: 10 % / Rfactor obs: 0.229 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.182
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_scbond_it10.492
X-RAY DIFFRACTIONc_mcangle_it2.812
X-RAY DIFFRACTIONc_scangle_it9.922.5
LS refinement shell
*PLUS
Lowest resolution: 2.53 Å

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