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- PDB-1j19: Crystal structure of the radxin FERM domain complexed with the IC... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1j19 | ||||||
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Title | Crystal structure of the radxin FERM domain complexed with the ICAM-2 cytoplasmic peptide | ||||||
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![]() | CELL ADHESION / protein-peptide complex | ||||||
Function / homology | ![]() 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 / plasma membrane => GO:0005886 / microvillus / cleavage furrow / positive regulation of G1/S transition of mitotic cell cycle / ruffle / cell adhesion molecule binding / 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 / actin binding / regulation of cell shape / midbody / cell adhesion / protein domain specific binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hamada, K. / Shimizu, T. / Yonemura, S. / Tsukita, S. / Tsukita, S. / Hakoshima, T. | ||||||
![]() | ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 84.9 KB | Display | ![]() |
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PDB format | ![]() | 63.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gc7S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | 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.) ![]() ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 1937.281 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.49 Å3/Da / Density % sol: 64.46 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→44.7 Å / Num. all: 599708 / Num. obs: 23153 / % possible obs: 100 % / Biso Wilson estimate: 41.7 Å2 |
Reflection shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 65.0264 Å2 / ksol: 0.328436 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→14.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
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Xplor file |
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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
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LS refinement shell | *PLUS Lowest resolution: 2.53 Å |