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Open data
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Basic information
Entry | Database: PDB / ID: 7ohi | ||||||
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Title | FCHO1-peptide-AP2 alpha ear complex | ||||||
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![]() | ENDOCYTOSIS / clathrin-mediated endocytosis (CME) / protein recycling / plasma membrane | ||||||
Function / homology | ![]() LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / AP-2 adaptor complex binding / VLDLR internalisation and degradation / Recycling pathway of L1 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization ...LDL clearance / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / WNT5A-dependent internalization of FZD4 / Trafficking of GluR2-containing AMPA receptors / Retrograde neurotrophin signalling / AP-2 adaptor complex binding / VLDLR internalisation and degradation / Recycling pathway of L1 / AP-2 adaptor complex / postsynaptic neurotransmitter receptor internalization / Cargo recognition for clathrin-mediated endocytosis / clathrin coat assembly / clathrin adaptor activity / Clathrin-mediated endocytosis / membrane coat / clathrin-dependent endocytosis / MHC class II antigen presentation / regulation of hematopoietic stem cell differentiation / protein serine/threonine kinase binding / clathrin-coated pit / vesicle-mediated transport / Neutrophil degranulation / phosphatidylinositol binding / secretory granule / intracellular protein transport / cytoplasmic side of plasma membrane / kinase binding / disordered domain specific binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / positive regulation of T cell activation / Clathrin-mediated endocytosis / T cell receptor signaling pathway / cytoplasmic vesicle / postsynapse / protein domain specific binding / protein-containing complex binding / protein kinase binding / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zaccai, N.R. / Kelly, B.T. / Evans, P.R. / Owen, D.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: FCHO controls AP2's initiating role in endocytosis through a PtdIns(4,5)P-dependent switch. Authors: Nathan R Zaccai / Zuzana Kadlecova / Veronica Kane Dickson / Kseniya Korobchevskaya / Jan Kamenicky / Oleksiy Kovtun / Perunthottathu K Umasankar / Antoni G Wrobel / Jonathan G G Kaufman / ...Authors: Nathan R Zaccai / Zuzana Kadlecova / Veronica Kane Dickson / Kseniya Korobchevskaya / Jan Kamenicky / Oleksiy Kovtun / Perunthottathu K Umasankar / Antoni G Wrobel / Jonathan G G Kaufman / Sally R Gray / Kun Qu / Philip R Evans / Marco Fritzsche / Filip Sroubek / Stefan Höning / John A G Briggs / Bernard T Kelly / David J Owen / Linton M Traub / ![]() ![]() ![]() ![]() ![]() Abstract: Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane- ...Clathrin-mediated endocytosis (CME) is the main mechanism by which mammalian cells control their cell surface proteome. Proper operation of the pivotal CME cargo adaptor AP2 requires membrane-localized Fer/Cip4 homology domain-only proteins (FCHO). Here, live-cell enhanced total internal reflection fluorescence-structured illumination microscopy shows that FCHO marks sites of clathrin-coated pit (CCP) initiation, which mature into uniform-sized CCPs comprising a central patch of AP2 and clathrin corralled by an FCHO/Epidermal growth factor potential receptor substrate number 15 (Eps15) ring. We dissect the network of interactions between the FCHO interdomain linker and AP2, which concentrates, orients, tethers, and partially destabilizes closed AP2 at the plasma membrane. AP2's subsequent membrane deposition drives its opening, which triggers FCHO displacement through steric competition with phosphatidylinositol 4,5-bisphosphate, clathrin, cargo, and CME accessory factors. FCHO can now relocate toward a CCP's outer edge to engage and activate further AP2s to drive CCP growth/maturation. #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012 Title: Towards automated crystallographic structure refinement with phenix.refine. Authors: Afonine, P.V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 145.3 KB | Display | ![]() |
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PDB format | ![]() | 92 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 459.9 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 20.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ofpC ![]() 7og1C ![]() 7ohoC ![]() 7ohzC ![]() 7oi5C ![]() 7oiqC ![]() 7oitC ![]() 7z5cC ![]() 1b9kS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 28048.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein/peptide | Mass: 2605.719 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-MES / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.6M Magnesium sulfate heptahydrate 0.1M MES pH 6.5. The crystal were subsequently cryo-protected with ~20% glycerol final. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→47.6 Å / Num. obs: 73320 / % possible obs: 95.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 18.81 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.017 / Rrim(I) all: 0.062 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 6.4 % / Rmerge(I) obs: 2.81 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 2558 / CC1/2: 0.253 / Rpim(I) all: 1.157 / Rrim(I) all: 3.054 / % possible all: 63.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1b9k Resolution: 1.41→44.4 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9259 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→44.4 Å
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Refine LS restraints |
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LS refinement shell |
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