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Yorodumi- PDB-4cc3: Complex of human Tuba C-terminal SH3 domain and Mena proline-rich... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4cc3 | ||||||
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Title | Complex of human Tuba C-terminal SH3 domain and Mena proline-rich peptide - H3 | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / TUBA / SRC HOMOLOGY 3 / SH3 DOMAIN / MENA / NDPP-1 / PROLINE- RICH PEPTIDE / ACTIN CYTOSKELETON / CORTICAL TENSION | ||||||
Function / homology | Function and homology information Signaling by ROBO receptors / actin polymerization-dependent cell motility / profilin binding / WW domain binding / Golgi stack / actin polymerization or depolymerization / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / stress fiber ...Signaling by ROBO receptors / actin polymerization-dependent cell motility / profilin binding / WW domain binding / Golgi stack / actin polymerization or depolymerization / regulation of small GTPase mediated signal transduction / CDC42 GTPase cycle / cilium assembly / stress fiber / cellular response to leukemia inhibitory factor / guanyl-nucleotide exchange factor activity / filopodium / actin filament organization / neural tube closure / axon guidance / SH3 domain binding / cell-cell junction / actin cytoskeleton / presynapse / lamellipodium / cell junction / actin binding / regulation of cell shape / actin cytoskeleton organization / cytoskeleton / neuron projection / intracellular signal transduction / focal adhesion / synapse / Golgi apparatus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Polle, L. / Rigano, L. / Julian, R. / Ireton, K. / Schubert, W.-D. | ||||||
Citation | Journal: Structure / Year: 2014 Title: Structural Details of Human Tuba Recruitment by Inlc of Listeria Monocytogenes Elucidate Bacterial Cell-Cell Spreading. Authors: Polle, L. / Rigano, L.A. / Julian, R. / Ireton, K. / Schubert, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4cc3.cif.gz | 137 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4cc3.ent.gz | 109.3 KB | Display | PDB format |
PDBx/mmJSON format | 4cc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/4cc3 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/4cc3 | HTTPS FTP |
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-Related structure data
Related structure data | 4cc2C 4cc4C 4cc7C 1zuuS 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 7712.617 Da / Num. of mol.: 4 / Fragment: C-TERMINAL SH3 DOMAIN, RESIDUES 1513-1577 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS / References: UniProt: Q6XZF7 #2: Protein/peptide | Mass: 1163.321 Da / Num. of mol.: 4 / Fragment: PROLINE-RICH PEPTIDE, RESIDUES 547-558 / Source method: obtained synthetically / Source: (synth.) MUS MUSCULUS (house mouse) / References: UniProt: Q03173 #3: Chemical | #4: Chemical | ChemComp-PE4 / | #5: Water | ChemComp-HOH / | Sequence details | THE FIRST TWO RESIDUES OF THE SEQUENCE GP ARE REMNANTS OF THE FUSION PROTEIN CLEAVAGE | |
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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: 2.6 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 2.5 M NACL, 0.1 M BIS-TRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2011 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 25648 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9 |
Reflection shell | Resolution: 1.97→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 95.5 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZUU Resolution: 1.97→34.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.721 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.781 Å2
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Refinement step | Cycle: LAST / Resolution: 1.97→34.33 Å
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Refine LS restraints |
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