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- PDB-6sct: Cryo-EM structure of the consensus triskelion hub of the clathrin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6sct | ||||||||||||
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Title | Cryo-EM structure of the consensus triskelion hub of the clathrin coat complex | ||||||||||||
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![]() | TRANSPORT PROTEIN / clathrin / coat protein / endocytosis / trafficking | ||||||||||||
Function / homology | ![]() clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / clathrin coat of coated pit / clathrin coat assembly / clathrin-coated endocytic vesicle / clathrin-coated vesicle / receptor-mediated endocytosis / ribosomal large subunit biogenesis / intracellular protein transport ...clathrin coat of trans-Golgi network vesicle / clathrin light chain binding / clathrin complex / clathrin coat of coated pit / clathrin coat assembly / clathrin-coated endocytic vesicle / clathrin-coated vesicle / receptor-mediated endocytosis / ribosomal large subunit biogenesis / intracellular protein transport / spindle / disordered domain specific binding / mitotic cell cycle / nucleolus / structural molecule activity / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.69 Å | ||||||||||||
![]() | Morris, K.L. / Cameron, A.D. / Sessions, R. / Smith, C.J. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM of multiple cage architectures reveals a universal mode of clathrin self-assembly. Authors: Kyle L Morris / Joseph R Jones / Mary Halebian / Shenping Wu / Michael Baker / Jean-Paul Armache / Amaurys Avila Ibarra / Richard B Sessions / Alexander D Cameron / Yifan Cheng / Corinne J Smith / ![]() ![]() Abstract: Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. ...Clathrin forms diverse lattice and cage structures that change size and shape rapidly in response to the needs of eukaryotic cells during clathrin-mediated endocytosis and intracellular trafficking. We present the cryo-EM structure and molecular model of assembled porcine clathrin, providing insights into interactions that stabilize key elements of the clathrin lattice, namely, between adjacent heavy chains, at the light chain-heavy chain interface and within the trimerization domain. Furthermore, we report cryo-EM maps for five different clathrin cage architectures. Fitting structural models to three of these maps shows that their assembly requires only a limited range of triskelion leg conformations, yet inherent flexibility is required to maintain contacts. Analysis of the protein-protein interfaces shows remarkable conservation of contact sites despite architectural variation. These data reveal a universal mode of clathrin assembly that allows variable cage architecture and adaptation of coated vesicle size and shape during clathrin-mediated vesicular trafficking or endocytosis. | ||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1 MB | Display | ![]() |
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PDB format | ![]() | 762.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 127.2 KB | Display | |
Data in CIF | ![]() | 195.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 0126MC ![]() 0114C ![]() 0115C ![]() 0116C ![]() 0118C ![]() 0120C ![]() 0121C ![]() 0122C ![]() 0123C ![]() 0124C ![]() 0125C M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 88.4 Data #1: Hub subparticles of the 28 mini coat [picked particles - multiframe - unprocessed] Data #2: Hub subparticles of the 32 sweet potato [picked particles - multiframe - unprocessed] Data #3: Hub subparticles of the 36 D6 barrel [picked particles - multiframe - unprocessed] Data #4: Hub subparticles of the 36 tennis ball [picked particles - multiframe - unprocessed] Data #5: Hub subparticles of the 37 big apple [picked particles - multiframe - unprocessed]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 191826.344 Da / Num. of mol.: 9 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 25218.500 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: clathrin cage triskelion hub consensus structure consisting of heavy and light chains Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.54 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE-PROPANE / Details: Ambient temperature and humidity |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 82111 X / Nominal defocus max: 2800 nm / Nominal defocus min: 1800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 69 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Sampling size: 14 µm / Width: 4096 / Height: 4096 |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 12785 / Details: Manual picking | ||||||||||||||||||||||||
Symmetry | Point symmetry: C3 (3 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313406 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient | ||||||||||||||||||||||||
Refine LS restraints |
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