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Yorodumi- PDB-7mt1: Crystal structure of Human Platelet-activating factor acetylhydro... -
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-Basic information
Entry | Database: PDB / ID: 7mt1 | ||||||
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Title | Crystal structure of Human Platelet-activating factor acetylhydrolase IB subunit beta (PAFAH1B1) | ||||||
Components | Platelet-activating factor acetylhydrolase IB subunit beta | ||||||
Keywords | PROTEIN BINDING / PAFAH1B1 / WD40 / WD-repeat protein / Structural Genomics / Structural Genomics Consortium / SGC | ||||||
Function / homology | Function and homology information 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 / microtubule organizing center organization / platelet activating factor metabolic process ...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 / microtubule organizing center organization / platelet activating factor metabolic process / acrosome assembly / radial glia-guided pyramidal neuron migration / cerebral cortex neuron differentiation / central region of growth cone / positive regulation of embryonic development / establishment of centrosome localization / reelin-mediated signaling pathway / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / astral microtubule / nuclear membrane disassembly / layer formation in cerebral cortex / auditory receptor cell development / vesicle transport along microtubule / stem cell division / positive regulation of dendritic spine morphogenesis / stereocilium / myeloid leukocyte migration / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / negative regulation of JNK cascade / osteoclast development / retrograde axonal transport / brain morphogenesis / motile cilium / nuclear migration / microtubule associated complex / kinesin complex / dynein intermediate chain binding / cochlea development / dynein complex binding / cytoplasmic microtubule / transmission of nerve impulse / cell leading edge / establishment of mitotic spindle orientation / germ cell development / dynactin binding / phospholipase binding / microtubule-based process / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of microtubule cytoskeleton organization / lipid catabolic process / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / JNK cascade / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / adult locomotory behavior / hippocampus development / RHO GTPases Activate Formins / phosphoprotein binding / neuron migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / kinetochore / cerebral cortex development / microtubule cytoskeleton organization / Separation of Sister Chromatids / nuclear envelope / Regulation of PLK1 Activity at G2/M Transition / negative regulation of neuron projection development / heparin binding / cell cortex / nuclear membrane / actin cytoskeleton organization / microtubule binding / chemical synaptic transmission / learning or memory / neuron projection / protein heterodimerization activity / centrosome / neuronal cell body / glutamatergic synapse / perinuclear region of cytoplasm / extracellular exosome / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Hutchinson, A. / Seitova, A. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Human Platelet-activating factor acetylhydrolase IB subunit beta (PAFAH1B1) Authors: Hutchinson, A. / Seitova, A. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mt1.cif.gz | 86.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mt1.ent.gz | 61.1 KB | Display | PDB format |
PDBx/mmJSON format | 7mt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7mt1_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 7mt1_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 7mt1_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | 7mt1_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mt/7mt1 ftp://data.pdbj.org/pub/pdb/validation_reports/mt/7mt1 | HTTPS FTP |
-Related structure data
Related structure data | 1vyhS S: Starting model for refinement |
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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
#1: Protein | Mass: 39014.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43034 | ||||
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#2: Chemical | ChemComp-GOL / | ||||
#3: Chemical | ChemComp-UNX / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.13 % / Mosaicity: 0.09 ° |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 18% PEG8K, 0.1M Tris pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 11, 2021 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→36.04 Å / Num. obs: 82396 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.015 / Rrim(I) all: 0.037 / Net I/σ(I): 22.5 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1vyh Resolution: 1.3→36.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.728 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.33 Å2 / Biso mean: 15.789 Å2 / Biso min: 8.26 Å2
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Refinement step | Cycle: final / Resolution: 1.3→36.03 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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