+Open data
-Basic information
Entry | Database: PDB / ID: 1vyh | ||||||
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Title | PAF-AH Holoenzyme: Lis1/Alfa2 | ||||||
Components |
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Keywords | HYDROLASE / LISSENCEPHALY / ACETYLHYDROLASE / PLATELET ACTIVACTING FACTOR / REGULATOR OF CYTOPLASMIC DYNEIN / CELL DIVISION / MITOSIS / NEUROGENESIS / CYTOSKELETON | ||||||
Function / homology | Function and homology information positive regulation of cellular component organization / platelet-activating factor acetyltransferase activity / corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding ...positive regulation of cellular component organization / platelet-activating factor acetyltransferase activity / corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase / acrosome assembly / 1-alkyl-2-acetylglycerophosphocholine esterase activity / radial glia-guided pyramidal neuron migration / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / microtubule organizing center organization / cerebral cortex neuron differentiation / central region of growth cone / positive regulation of embryonic development / neutrophil degranulation / reelin-mediated signaling pathway / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / establishment of centrosome localization / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / astral microtubule / RHO GTPases Activate Formins / layer formation in cerebral cortex / nuclear membrane disassembly / Separation of Sister Chromatids / auditory receptor cell development / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of dendritic spine morphogenesis / AURKA Activation by TPX2 / vesicle transport along microtubule / Regulation of PLK1 Activity at G2/M Transition / stem cell division / stereocilium / myeloid leukocyte migration / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / negative regulation of JNK cascade / retrograde axonal transport / brain morphogenesis / motile cilium / nuclear migration / osteoclast development / microtubule associated complex / Neutrophil degranulation / regulation of postsynapse organization / kinesin complex / dynein intermediate chain binding / dynein complex binding / cochlea development / transmission of nerve impulse / cytoplasmic microtubule / cell leading edge / germ cell development / establishment of mitotic spindle orientation / positive regulation of macroautophagy / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / microtubule-based process / lipid catabolic process / regulation of microtubule cytoskeleton organization / axon cytoplasm / JNK cascade / positive regulation of mitotic cell cycle / adult locomotory behavior / establishment of localization in cell / hippocampus development / phosphoprotein binding / brain development / neuron migration / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / lipid metabolic process / kinetochore / cerebral cortex development / fibrillar center / microtubule cytoskeleton organization / microtubule cytoskeleton / cell migration / negative regulation of neuron projection development / nuclear envelope / cell cortex / growth cone / actin cytoskeleton organization / chemical synaptic transmission / microtubule binding / spermatogenesis Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Tarricone, C. / Perrina, F. / Monzani, S. / Massimiliano, L. / Knapp, S. / Tsai, L.-H. / Derewenda, Z.S. / Musacchio, A. | ||||||
Citation | Journal: Neuron / Year: 2004 Title: Coupling Paf Signaling to Dynein Regulation: Structure of Lis1 in Complex with Paf-Acetylhydrolase. Authors: Tarricone, C. / Perrina, F. / Monzani, S. / Massimiliano, L. / Kim, M.H. / Derewenda, Z.S. / Knapp, S. / Tsai, L.-H. / Musacchio, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vyh.cif.gz | 985 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vyh.ent.gz | 806.3 KB | Display | PDB format |
PDBx/mmJSON format | 1vyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/1vyh ftp://data.pdbj.org/pub/pdb/validation_reports/vy/1vyh | HTTPS FTP |
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-Related structure data
Related structure data | 1fxwS 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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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 25600.264 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q29459, UniProt: P68402*PLUS, 1-alkyl-2-acetylglycerophosphocholine esterase #2: Protein | Mass: 46786.133 Da / Num. of mol.: 10 / Fragment: C-TERM BETA-PROPELLER, RESIDUES 1-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Organ: BRAIN / Plasmid: PFASTBAC-HTB / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P63005 Compound details | CATALYTIC ACTIVITY: 2-ACETYL-1-ALKYL-SN-GLYCERO-3-PHOSPHOCHOLINE + THE CATALYTIC ACTIVITY OF THE ...CATALYTIC ACTIVITY: 2-ACETYL-1-ALKYL-SN-GLYCERO-3-PHOSPHOCHO | |
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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: 3.51 Å3/Da / Density % sol: 64.92 % Description: 10 TRANSLATIONS WERE PERFORMED ON THE SAME CRYSTAL |
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Crystal grow | pH: 8.5 / Details: 16% PEG8K 0.2M KSCN, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 21, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9756 Å / Relative weight: 1 |
Reflection | Resolution: 3.391→30 Å / Num. obs: 139752 / % possible obs: 96.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 3.39→3.52 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FXW Resolution: 3.4→200 Å / SU B: 31.44 / SU ML: 0.523 / Cross valid method: THROUGHOUT / ESU R Free: 0.608
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Displacement parameters | Biso mean: 17.425 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→200 Å
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