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- PDB-3aa1: Crystal structure of Actin capping protein in complex with the Cp... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3aa1 | ||||||
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Title | Crystal structure of Actin capping protein in complex with the Cp-binding motif derived from CKIP-1 | ||||||
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![]() | PROTEIN BINDING / ACTIN CAPPING PROTEIN / BARBED END REGULATION / CARMIL FAMILY PROTEIN / CONFORMATIONAL CHANGE / CELL MOTILITY / Actin capping / Actin-binding / Cytoskeleton / Cell membrane / Tumor suppressor | ||||||
Function / homology | ![]() muscle cell projection membrane / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / lamellipodium morphogenesis / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / WASH complex ...muscle cell projection membrane / Advanced glycosylation endproduct receptor signaling / RHOD GTPase cycle / RHOF GTPase cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / lamellipodium morphogenesis / COPI-mediated anterograde transport / Factors involved in megakaryocyte development and platelet production / WASH complex / : / F-actin capping protein complex / myoblast migration / negative regulation of filopodium assembly / cell junction assembly / myoblast fusion / barbed-end actin filament capping / actin polymerization or depolymerization / regulation of cell morphogenesis / regulation of lamellipodium assembly / lamellipodium assembly / cortical cytoskeleton / brush border / cytoskeleton organization / hippocampal mossy fiber to CA3 synapse / Schaffer collateral - CA1 synapse / cell morphogenesis / ruffle membrane / Z disc / actin filament binding / lamellipodium / regulation of cell shape / actin cytoskeleton organization / postsynaptic density / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Takeda, S. / Minakata, S. / Narita, A. / Kitazawa, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y. | ||||||
![]() | ![]() Title: Two distinct mechanisms for actin capping protein regulation--steric and allosteric inhibition Authors: Takeda, S. / Minakata, S. / Koike, R. / Kawahata, I. / Narita, A. / Kitazawa, M. / Ota, M. / Yamakuni, T. / Maeda, Y. / Nitanai, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.5 KB | Display | ![]() |
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PDB format | ![]() | 100.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 456.5 KB | Display | ![]() |
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Full document | ![]() | 464.8 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 38.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3aa0C ![]() 3aa6C ![]() 3aa7C ![]() 3aaaC ![]() 1iznS S: Starting model for refinement C: citing same article ( |
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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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Details | THE ORIGOMETRIC STATE OF THE ACTIN CAPPING PROTEIN IS A HETERO DIMER COMPOSE OF SUBUNIT A (CHAIN A) AND SUBUNIT B (CHAIN B) IN VIVO AND IN VITRO. |
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Components
#1: Protein | Mass: 33001.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Protein | Mass: 27473.070 Da / Num. of mol.: 1 / Mutation: residues 244-277 deletion mutation Source method: isolated from a genetically manipulated source Details: BETA TENTACLE DELETION / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Protein/peptide | Mass: 2709.078 Da / Num. of mol.: 1 / Fragment: CP-BINDING MOTIF, recidues 148-170 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / Source: (synth.) ![]() | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 40.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 17.5% PEG 400, 30MM BACL2, 100MM MES-NAOH, PH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 11, 2009 / Details: mirrors |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 40661 / % possible obs: 97.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.9 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.66 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.41 / Num. unique all: 3337 / % possible all: 81.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1IZN Resolution: 1.9→43.36 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.91 / SU B: 4.35 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.181 / 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: 33.816 Å2
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Refine analyze | Luzzati coordinate error obs: 0.236 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→43.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.902→1.952 Å / Total num. of bins used: 20
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