+Open data
-Basic information
Entry | Database: PDB / ID: 1mb8 | ||||||
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Title | Crystal Structure of the actin binding domain of plectin | ||||||
Components | Plectin | ||||||
Keywords | STRUCTURAL PROTEIN / CALPONIN HOMOLOGY DOMAIN / ACTIN BINDING DOMAIN / INTEGRIN BETA4 HEMIDESMOSOMES / CYTOSKELETON / EPIDERMOLYSIS BULLOSA | ||||||
Function / homology | Function and homology information protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / : ...protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / : / regulation of vascular permeability / intermediate filament cytoskeleton organization / dystroglycan binding / cellular response to hydrostatic pressure / fibroblast migration / costamere / T cell chemotaxis / cellular response to fluid shear stress / peripheral nervous system myelin maintenance / cardiac muscle cell development / myoblast differentiation / adherens junction organization / intermediate filament cytoskeleton / intermediate filament / response to food / structural constituent of muscle / ankyrin binding / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / nucleus organization / keratinocyte development / transmission of nerve impulse / brush border / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / skeletal muscle fiber development / respiratory electron transport chain / mitochondrion organization / wound healing / protein localization / cell morphogenesis / multicellular organism growth / structural constituent of cytoskeleton / sarcolemma / Z disc / cellular response to mechanical stimulus / : / actin filament binding / myelin sheath / gene expression / mitochondrial outer membrane / cadherin binding / axon / focal adhesion / dendrite / perinuclear region of cytoplasm / RNA binding / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | de Pereda, J.M. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structural and Functional Analysis of the Actin Binding Domain of Plectin Suggests Alternative Mechanisms for Binding to F-Actin and Integrin Beta4 Authors: Garcia-Alvarez, B. / Bobkov, A. / Sonnenberg, A. / de Pereda, J.M. | ||||||
History |
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Remark 999 | SEQUENCE AUTHOR INFORMED THAT THE HWRAE INSERTION HAS BEEN DESCRIBED IN MOUSE. AUTHOR ALSO INFORMED ...SEQUENCE AUTHOR INFORMED THAT THE HWRAE INSERTION HAS BEEN DESCRIBED IN MOUSE. AUTHOR ALSO INFORMED THAT RESIDUE ASN 149 IS CORRECT AND THAT THE CONFLICT ON THIS POSITION IS LIKELY DUE TO POLYMORPHISM. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mb8.cif.gz | 64.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mb8.ent.gz | 47.7 KB | Display | PDB format |
PDBx/mmJSON format | 1mb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/1mb8 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/1mb8 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28444.568 Da / Num. of mol.: 1 / Fragment: Residues 59-293 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15149 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.2 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 24, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→35 Å / Num. all: 12571 / Num. obs: 11486 / % possible obs: 91.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.9 Å2 |
Reflection shell | Resolution: 2.15→2.28 Å / % possible all: 69.2 |
Reflection | *PLUS Lowest resolution: 32 Å / % possible obs: 91.2 % / Num. measured all: 42883 / Rmerge(I) obs: 0.082 |
Reflection shell | *PLUS Lowest resolution: 2.23 Å / % possible obs: 61.4 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 3.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→31.11 Å / Rfactor Rfree error: 0.009 / 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: 48.2332 Å2 / ksol: 0.310086 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→31.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.28 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 32 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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