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Yorodumi- PDB-2pbd: Ternary complex of profilin-actin with the poly-PRO-GAB domain of... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pbd | ||||||
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Title | Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP* | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Ternary complex / profilin / actin / VASP / Poly-Proline / Loading Poly-Pro Site / GAB domain | ||||||
Function / homology | Function and homology information synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / profilin binding / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / Cell-extracellular matrix interactions ...synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / profilin binding / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / Signaling by ROBO receptors / regulation of actin filament polymerization / Cell-extracellular matrix interactions / actin polymerization or depolymerization / positive regulation of ATP-dependent activity / filopodium membrane / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / positive regulation of actin filament polymerization / tropomyosin binding / positive regulation of epithelial cell migration / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / lamellipodium membrane / striated muscle thin filament / actin filament bundle assembly / Generation of second messenger molecules / skeletal muscle myofibril / actin monomer binding / bicellular tight junction / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / filopodium / neural tube closure / axon guidance / actin filament / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / modulation of chemical synaptic transmission / small GTPase binding / SH3 domain binding / calcium-dependent protein binding / actin cytoskeleton / Platelet degranulation / lamellipodium / actin binding / cell cortex / cell body / actin cytoskeleton organization / protein homotetramerization / blood microparticle / cytoskeleton / protein stabilization / hydrolase activity / cadherin binding / protein domain specific binding / focal adhesion / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / magnesium ion binding / RNA binding / extracellular exosome / ATP binding / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.501 Å | ||||||
Authors | Ferron, F. / Rebowski, G. / Dominguez, R. | ||||||
Citation | Journal: Embo J. / Year: 2007 Title: Structural basis for the recruitment of profilin-actin complexes during filament elongation by Ena/VASP Authors: Ferron, F. / Rebowski, G. / Lee, S.H. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pbd.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pbd.ent.gz | 106.7 KB | Display | PDB format |
PDBx/mmJSON format | 2pbd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/2pbd ftp://data.pdbj.org/pub/pdb/validation_reports/pb/2pbd | HTTPS FTP |
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-Related structure data
Related structure data | 2pavSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 2 types, 2 molecules AP
#1: Protein | Mass: 42109.973 Da / Num. of mol.: 1 / Fragment: residues 1-377 / Source method: isolated from a natural source / Details: gene ACTA1, ACTA / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscle / References: UniProt: P68135 |
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#2: Protein | Mass: 14940.021 Da / Num. of mol.: 1 / Fragment: residues 2-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PFN1 / Organ: brain / Plasmid: pET29 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07737 |
-Protein/peptide , 1 types, 1 molecules V
#3: Protein/peptide | Mass: 3875.391 Da / Num. of mol.: 1 / Fragment: VASP Loading Poly-Pro Site and GAB domain / Source method: obtained synthetically Details: This sequence occurs naturally in humans, gene VASP References: UniProt: P50552 |
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-Non-polymers , 3 types, 734 molecules
#4: Chemical | ChemComp-CA / |
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#5: Chemical | ChemComp-ATP / |
#6: 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: 2.01 Å3/Da / Density % sol: 38.83 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 150mM DL-malic acid pH 7.0, 18% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2006 / Details: mirrors |
Radiation | Monochromator: Bent conical Si-mirror (Rh coated) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9002 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 75393 / Num. obs: 75393 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 10.87 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 9 / Num. unique all: 7487 / Rsym value: 0.293 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PAV Resolution: 1.501→31.77 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.249 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.076 / 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: 10.847 Å2
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Refinement step | Cycle: LAST / Resolution: 1.501→31.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.501→1.54 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 | Refine-ID: X-RAY DIFFRACTION / Selection: ALL
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