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- PDB-1hfa: CALM-N N-terminal domain of clathrin assembly lymphoid myeloid le... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1hfa | ||||||
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Title | CALM-N N-terminal domain of clathrin assembly lymphoid myeloid leukaemia protein, PI(4,5)P2 complex | ||||||
![]() | CLATHRIN ASSEMBLY PROTEIN SHORT FORM | ||||||
![]() | ENDOCYTOSIS / ADAPTOR | ||||||
Function / homology | ![]() membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / positive regulation of amyloid precursor protein catabolic process / 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 ...membrane bending / RND3 GTPase cycle / vesicle cargo loading / endosome to plasma membrane transport vesicle / positive regulation of amyloid precursor protein catabolic process / 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 / parallel fiber to Purkinje cell synapse / negative regulation of protein localization to plasma membrane / dendrite morphogenesis / regulation of synaptic vesicle endocytosis / clathrin-coated vesicle / neurofibrillary tangle / endosomal transport / low-density lipoprotein particle receptor binding / positive regulation of axonogenesis / clathrin binding / positive regulation of amyloid-beta formation / hemopoiesis / regulation of endocytosis / synaptic vesicle endocytosis / clathrin-coated pit / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / axonogenesis / SNARE binding / receptor-mediated endocytosis / Schaffer collateral - CA1 synapse / tau protein binding / receptor internalization / small GTPase binding / multicellular organismal-level iron ion homeostasis / SH3 domain binding / endocytosis / regulation of protein localization / synaptic vesicle / presynaptic membrane / postsynapse / postsynaptic membrane / intracellular iron ion homeostasis / vesicle / postsynaptic density / learning or memory / early endosome / endosome / negative regulation of gene expression / neuronal cell body / positive regulation of DNA-templated transcription / Golgi apparatus / cell surface / identical protein binding / membrane / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ford, M.G.J. / Evans, P.R. / McMahon, H.T. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.7 KB | Display | ![]() |
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PDB format | ![]() | 51.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 483.1 KB | Display | ![]() |
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Full document | ![]() | 494.1 KB | Display | |
Data in XML | ![]() | 12.5 KB | Display | |
Data in CIF | ![]() | 18.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1hf8SC ![]() 1hg2C ![]() 1hg5C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | BIOLOGICAL_UNIT: MONOMERTHIS DIMERIC ARRANGEMENT IS THE RESULT OF TIGHT CRYSTALPACKING. |
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Components
#1: Protein | Mass: 32865.789 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PIO / [( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60 % | ||||||||||||||||||||
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Crystal grow | 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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 23, 2000 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 2→66 Å / Num. obs: 26075 / % possible obs: 100 % / Observed criterion σ(I): 6 / Redundancy: 7.1 % / Biso Wilson estimate: 43 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.104 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 1.5 / Rsym value: 1.153 / % possible all: 100 |
Reflection | *PLUS % possible obs: 100 % |
Reflection shell | *PLUS % possible obs: 100 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 1HF8 Resolution: 2→65.94 Å / SU B: 7.171 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 43.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2→65.94 Å
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Software | *PLUS Name: REFMAC / Version: 5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.19844 / Rfactor Rfree: 0.23012 / Rfactor Rwork: 0.19678 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 43.712 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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