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Yorodumi- PDB-3kbu: Crystal structure of the ankyrin binding domain of human erythroi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kbu | ||||||
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Title | Crystal structure of the ankyrin binding domain of human erythroid beta spectrin (repeats 13-15) in complex with the spectrin binding domain of human erythroid ankyrin (ZU5-ANK), EMTS derivative | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / complex / spectrin / spectrin repeat / three helix bundle / ankyrin binding / disease mutation / ankyrin / ZU5 / beta sandwich / spectrin binding / cytoskeleton / membrane skeleton / Actin capping / Actin-binding / Elliptocytosis / Hereditary hemolytic anemia / Phosphoprotein / Alternative promoter usage / ANK repeat / Lipoprotein / Membrane / Sarcoplasmic reticulum | ||||||
Function / homology | Function and homology information spectrin / spectrin-associated cytoskeleton / positive regulation of organelle organization / modification of postsynaptic actin cytoskeleton / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / ankyrin-1 complex / Neurofascin interactions / CHL1 interactions / cytoskeletal anchor activity ...spectrin / spectrin-associated cytoskeleton / positive regulation of organelle organization / modification of postsynaptic actin cytoskeleton / maintenance of epithelial cell apical/basal polarity / NrCAM interactions / ankyrin-1 complex / Neurofascin interactions / CHL1 interactions / cytoskeletal anchor activity / actin filament capping / M band / Interaction between L1 and Ankyrins / ankyrin binding / spectrin binding / cortical actin cytoskeleton / exocytosis / axolemma / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / cytoskeleton organization / NCAM signaling for neurite out-growth / sarcoplasmic reticulum / cell projection / protein localization to plasma membrane / sarcolemma / cytoplasmic side of plasma membrane / structural constituent of cytoskeleton / Z disc / actin filament binding / actin cytoskeleton / cell junction / actin binding / ATPase binding / actin cytoskeleton organization / RAF/MAP kinase cascade / postsynaptic membrane / postsynapse / basolateral plasma membrane / protein phosphatase binding / transmembrane transporter binding / cytoskeleton / neuron projection / glutamatergic synapse / structural molecule activity / enzyme binding / cell surface / signal transduction / protein-containing complex / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.75 Å | ||||||
Authors | Ipsaro, J.J. / Mondragon, A. | ||||||
Citation | Journal: Blood / Year: 2010 Title: Structural basis for spectrin recognition by ankyrin. Authors: Ipsaro, J.J. / Mondragon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbu.cif.gz | 188 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbu.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 3kbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbu ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbu | HTTPS FTP |
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-Related structure data
Related structure data | 3kbtC 3f57S 3f59S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 37219.352 Da / Num. of mol.: 2 / Fragment: UNP residues 1583-1906 / Mutation: E1680C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPTB, SPTB1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11277 #2: Protein | Mass: 17885.594 Da / Num. of mol.: 2 / Fragment: UNP residues 911-1068 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ANK, ANK1 / Plasmid: pICANTE / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P16157 #3: Chemical | ChemComp-HG / Sequence details | EL TO DV SEQUENCE CONFLICT IN UNP ENTRY P16157 | |
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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: 2.78 Å3/Da / Density % sol: 55.74 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Protein complex at 7.5 mg/mL mixed 1:1 with 0.05 M MES pH 6.5, 0.2 M ammonium acetate, 0.01 M calcium chloride, 10% PEG-4000, VAPOR DIFFUSION, HANGING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 7, 2008 |
Radiation | Monochromator: Diamond laue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. all: 32653 / Num. obs: 32570 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 27.8 Å2 / Rsym value: 0.058 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.75→2.87 Å / Redundancy: 5 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.288 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SAD Starting model: PDB entries 3F57, 3F59 Resolution: 2.75→37.82 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.889 / SU B: 30.686 / SU ML: 0.295 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.108 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.628 Å2
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Refinement step | Cycle: LAST / Resolution: 2.75→37.82 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.75→2.821 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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