+Open data
-Basic information
Entry | Database: PDB / ID: 1ni2 | ||||||
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Title | Structure of the active FERM domain of Ezrin | ||||||
Components | Ezrin | ||||||
Keywords | STRUCTURAL PROTEIN / FERM / KEYSTONE / UBIQUITIN-LIKE DOMAIN / ACYL-COA-LIKE DOMAIN / PH/PTB-LIKE DOMAIN | ||||||
Function / homology | Function and homology information terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization ...terminal web assembly / intestinal D-glucose absorption / protein localization to cell cortex / establishment or maintenance of apical/basal cell polarity / regulation of microvillus length / regulation of organelle assembly / microvillus assembly / positive regulation of early endosome to late endosome transport / membrane to membrane docking / establishment of centrosome localization / cortical microtubule organization / negative regulation of p38MAPK cascade / Netrin-1 signaling / uropod / astral microtubule organization / postsynaptic actin cytoskeleton organization / positive regulation of protein localization to early endosome / filopodium assembly / positive regulation of multicellular organism growth / protein-containing complex localization / sphingosine-1-phosphate receptor signaling pathway / establishment of endothelial barrier / S100 protein binding / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / protein kinase A binding / negative regulation of interleukin-2 production / microvillus membrane / negative regulation of T cell receptor signaling pathway / leukocyte cell-cell adhesion / cortical cytoskeleton / Recycling pathway of L1 / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / plasma membrane raft / actin filament bundle assembly / microvillus / brush border / immunological synapse / protein kinase A signaling / cellular response to cAMP / ruffle / cell adhesion molecule binding / ciliary basal body / filopodium / cell projection / actin filament / cell periphery / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / adherens junction / negative regulation of ERK1 and ERK2 cascade / receptor internalization / fibrillar center / ruffle membrane / positive regulation of protein catabolic process / disordered domain specific binding / actin filament binding / actin cytoskeleton / apical part of cell / actin binding / ATPase binding / regulation of cell shape / actin cytoskeleton organization / microtubule binding / basolateral plasma membrane / vesicle / endosome / cadherin binding / apical plasma membrane / protein domain specific binding / focal adhesion / positive regulation of gene expression / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / RNA binding / extracellular exosome / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Smith, W.J. / Nassar, N. / Bretscher, A.P. / Cerione, R.A. / Karplus, P.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structure of the Active N-terminal Domain of Ezrin. CONFORMATIONAL AND MOBILITY CHANGES IDENTIFY KEYSTONE INTERACTIONS. Authors: Smith, W.J. / Nassar, N. / Bretscher, A.P. / Cerione, R.A. / Karplus, P.A. | ||||||
History |
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Remark 600 | Heterogen compared to the published model this has 11 less waters. The author requested the removal ...Heterogen compared to the published model this has 11 less waters. The author requested the removal of these waters because they were in unreasonable positions. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ni2.cif.gz | 139.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ni2.ent.gz | 109.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ni2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ni/1ni2 ftp://data.pdbj.org/pub/pdb/validation_reports/ni/1ni2 | HTTPS FTP |
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-Related structure data
Related structure data | 1ef1S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34948.395 Da / Num. of mol.: 2 / Fragment: residue 1-296 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VIL2 / Plasmid: PQE16 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P15311 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 48.79 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 10% PEG 2K, 10% GLYCEROL, 5% ISOPROPANOL, TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8.1 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.901 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 8, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.27 Å / Num. obs: 27658 / % possible obs: 89.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Biso Wilson estimate: 43 Å2 / Limit h max: 20 / Limit h min: -21 / Limit k max: 46 / Limit k min: -21 / Limit l max: 28 / Limit l min: 0 / Observed criterion F max: 1312241.54 / Observed criterion F min: 4.7 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.3→2.4 Å / % possible all: 89.3 |
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 26 Å / Num. obs: 27498 / Num. measured all: 183710 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 77.2 % / Rmerge(I) obs: 0.256 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb is 1EF1 Resolution: 2.3→25.86 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 51.9763 Å2 / ksol: 0.318812 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.11 Å2 / Biso mean: 57.79 Å2 / Biso min: 17.24 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→25.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 26 Å / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.229 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.364 / Rfactor Rwork: 0.399 |