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Yorodumi- PDB-1hg2: CALM-N N-terminal domain of clathrin assembly lymphoid myeloid le... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hg2 | ||||||
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Title | CALM-N N-terminal domain of clathrin assembly lymphoid myeloid leukaemia protein, Inositol(4,5)P2 complex | ||||||
Components | CLATHRIN ASSEMBLY PROTEIN SHORT FORM | ||||||
Keywords | ENDOCYTOSIS / ADAPTOR | ||||||
Function / homology | Function and homology information membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / positive regulation of amyloid precursor protein catabolic process / postsynaptic endocytic zone / synaptic vesicle budding from presynaptic endocytic zone membrane / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering ...membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / positive regulation of amyloid precursor protein catabolic process / postsynaptic endocytic zone / synaptic vesicle budding from presynaptic endocytic zone membrane / 1-phosphatidylinositol binding / regulation of terminal button organization / positive regulation of synaptic vesicle clustering / regulation of protein transport / extrinsic component of presynaptic endocytic zone membrane / regulation of synaptic vesicle transport / Golgi Associated Vesicle Biogenesis / clathrin heavy chain binding / amyloid-beta clearance by transcytosis / clathrin coat of coated pit / regulation of vesicle size / synaptic vesicle maturation / negative regulation of protein localization to cell surface / negative regulation of receptor-mediated endocytosis / clathrin coat assembly / Cargo recognition for clathrin-mediated endocytosis / positive regulation of synaptic vesicle endocytosis / Clathrin-mediated endocytosis / vesicle budding from membrane / positive regulation of dendrite extension / clathrin-dependent endocytosis / regulation of amyloid precursor protein catabolic process / negative regulation of protein localization to plasma membrane / parallel fiber to Purkinje cell synapse / dendrite morphogenesis / regulation of synaptic vesicle endocytosis / clathrin-coated vesicle / neurofibrillary tangle / endosomal transport / low-density lipoprotein particle receptor binding / clathrin binding / positive regulation of axonogenesis / positive regulation of amyloid-beta formation / regulation of endocytosis / hemopoiesis / synaptic vesicle endocytosis / clathrin-coated pit / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / receptor-mediated endocytosis / axonogenesis / SNARE binding / tau protein binding / Schaffer collateral - CA1 synapse / receptor internalization / small GTPase binding / multicellular organismal-level iron ion homeostasis / SH3 domain binding / endocytosis / regulation of protein localization / synaptic vesicle / presynaptic membrane / postsynaptic membrane / intracellular iron ion homeostasis / vesicle / postsynapse / learning or memory / endosome / postsynaptic density / early endosome / negative regulation of gene expression / neuronal cell body / positive regulation of DNA-templated transcription / cell surface / Golgi apparatus / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ford, M.G.J. / Evans, P.R. / McMahon, H.T. | ||||||
Citation | Journal: Science / Year: 2001 Title: Simultaneous Binding of Ptdins(4,5)P2 and Clathrin by Ap180 in the Nucleation of Clathrin Lattices on Membranes Authors: Ford, M.G.J. / Pearse, B.M.F. / Higgins, M.K. / Vallis, Y. / Owen, D.J. / Gibson, A. / Hopkins, C.R. / Evans, P.R. / Mcmahon, H.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hg2.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hg2.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hg2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hg2_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 1hg2_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 1hg2_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 1hg2_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/1hg2 ftp://data.pdbj.org/pub/pdb/validation_reports/hg/1hg2 | HTTPS FTP |
-Related structure data
Related structure data | 1hf8SC 1hfaC 1hg5C 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
#1: Protein | Mass: 32865.789 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN RESIDUES 1-289 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PGEX4T2 / Gene (production host): CALM-N / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O55011, UniProt: O55012*PLUS |
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#2: Chemical | ChemComp-IP2 / |
#3: 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: 3.08 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, PH 7.5, 12% PEG 8K, 8% ETHYLENE GLYCOL CRYSTALS SOAKED IN 1MM LIGAND FOR 1 HOUR | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2000 |
Radiation | Monochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→37 Å / Num. obs: 25871 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 7.2 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.126 / Rsym value: 0.126 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 1.958 / Mean I/σ(I) obs: 1.3 / Rsym value: 1.958 / % possible all: 99.9 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1HF8 Resolution: 2→65.94 Å / SU B: 6.97015 / SU ML: 0.18832 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15442 / ESU R Free: 0.13478 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SCALING DETAILS BABINET"S PRINCIPLE FOR SCALING HAS BEEN USED BULK SOLVENT CORRECTION BASED ON CONSTANT VALUE HAS BEEN U PARAMETERS FOR MASK ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS SCALING DETAILS BABINET"S PRINCIPLE FOR SCALING HAS BEEN USED BULK SOLVENT CORRECTION BASED ON CONSTANT VALUE HAS BEEN U PARAMETERS FOR MASK CALCULATION VDW PROB RADII = 1.40 ION PROB RADII = 0.80 SHRINKAGE RADII = 0.80
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Displacement parameters | Biso mean: 43.942 Å2
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Refinement step | Cycle: LAST / Resolution: 2→65.94 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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