+Open data
-Basic information
Entry | Database: PDB / ID: 6wcj | ||||||
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Title | Asymmetric vertex of the clathrin minicoat cage | ||||||
Components |
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Keywords | ENDOCYTOSIS / Clathrin coated vesicle / clathrin heavy chain / clathrin light chain / clathrin cage | ||||||
Function / homology | Function and homology information postsynaptic endocytic zone cytoplasmic component / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / clathrin vesicle coat ...postsynaptic endocytic zone cytoplasmic component / Retrograde neurotrophin signalling / Recycling pathway of L1 / WNT5A-dependent internalization of FZD4 / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / LDL clearance / Gap junction degradation / Formation of annular gap junctions / Golgi Associated Vesicle Biogenesis / clathrin vesicle coat / RHOU GTPase cycle / RHOV GTPase cycle / clathrin coat of trans-Golgi network vesicle / Lysosome Vesicle Biogenesis / clathrin light chain binding / negative regulation of hyaluronan biosynthetic process / clathrin complex / clathrin coat / MHC class II antigen presentation / VLDLR internalisation and degradation / clathrin heavy chain binding / clathrin coat of coated pit / Cargo recognition for clathrin-mediated endocytosis / clathrin coat disassembly / clathrin coat assembly / clathrin-coated endocytic vesicle / membrane coat / Clathrin-mediated endocytosis / clathrin-dependent endocytosis / arrestin family protein binding / receptor-mediated endocytosis / intracellular protein transport / synaptic vesicle membrane / autophagy / spindle / disordered domain specific binding / melanosome / mitotic cell cycle / protein domain specific binding / cell division / structural molecule activity / mitochondrion / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å | ||||||
Authors | Paraan, M. / Mendez, J. / Sharum, S. / Kurtin, D. / He, H. / Stagg, S. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2020 Title: The structures of natively assembled clathrin-coated vesicles. Authors: Mohammadreza Paraan / Joshua Mendez / Savanna Sharum / Danielle Kurtin / Huan He / Scott M Stagg / Abstract: Clathrin-coated vesicles mediate trafficking of proteins and nutrients in the cell and between organelles. Proteins included in the clathrin-coated vesicles (CCVs) category include clathrin heavy ...Clathrin-coated vesicles mediate trafficking of proteins and nutrients in the cell and between organelles. Proteins included in the clathrin-coated vesicles (CCVs) category include clathrin heavy chain (CHC), clathrin light chain (CLC), and a variety of adaptor protein complexes. Much is known about the structures of the individual CCV components, but data are lacking about the structures of the fully assembled complexes together with membrane and in complex with cargo. Here, we determined the structures of natively assembled CCVs in a variety of geometries. We show that the adaptor β2 appendages crosslink adjacent CHC β-propellers and that the appendage densities are enriched in CCV hexagonal faces. We resolve how adaptor protein 2 and other associated factors in hexagonal faces form an assembly hub with an extensive web of interactions between neighboring β-propellers and propose a structural model that explains how adaptor binding can direct the formation of pentagonal and hexagonal faces. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6wcj.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6wcj.ent.gz | 760.1 KB | Display | PDB format |
PDBx/mmJSON format | 6wcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wcj_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6wcj_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6wcj_validation.xml.gz | 141.5 KB | Display | |
Data in CIF | 6wcj_validation.cif.gz | 209.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wc/6wcj ftp://data.pdbj.org/pub/pdb/validation_reports/wc/6wcj | HTTPS FTP |
-Related structure data
Related structure data | 21611MC M: map data used to model this data 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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-Components
#1: Antibody | Mass: 191800.312 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P49951 #2: Protein | Mass: 25109.396 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P04975 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Natively assembled clathrin coated vesicles / Type: COMPLEX / Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Source (natural) | Organism: Bos taurus (cattle) / Organ: brain | ||||||||||||||||||||
Buffer solution | pH: 6.7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid type: C-flat-2/2 4C | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 35000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 800 |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 360000 Details: These are subparticle images that were extracted from particle images. Each minicoat particle has 24 asymmetric vertices. From a total of 15000 minicoat particles, 360000 vertex subparticles ...Details: These are subparticle images that were extracted from particle images. Each minicoat particle has 24 asymmetric vertices. From a total of 15000 minicoat particles, 360000 vertex subparticles were extracted. The position of subparticles was calculated by the localized reconstruction script in scipion, and the subparticle images were extracted with RELION extraction tools. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 305413 Details: After the final refinement in cisTEM, half-maps were generated in cisTEM and the FSC was calculated with EMAN FSC tools. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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Atomic model building | Accession code: 6SCT / Initial refinement model-ID: 1 / PDB-ID: 6SCT / Source name: PDB / Type: experimental model
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Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.06 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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