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Open data
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Basic information
Entry | Database: PDB / ID: 6zga | |||||||||
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Title | COPII on membranes, inner coat | |||||||||
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![]() | PROTEIN TRANSPORT / SECRETION / TRAFFICKING | |||||||||
Function / homology | ![]() Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat ...Antigen Presentation: Folding, assembly and peptide loading of class I MHC / Cargo concentration in the ER / regulation of COPII vesicle coating / positive regulation of ER to Golgi vesicle-mediated transport / mitochondria-associated endoplasmic reticulum membrane contact site / COPII-mediated vesicle transport / nuclear envelope organization / COPII-coated vesicle cargo loading / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / mitochondrial fission / signal sequence binding / mitochondrial membrane organization / reticulophagy / fungal-type vacuole membrane / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / SNARE binding / macroautophagy / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / mitochondrion / zinc ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Zanetti, G. / Hutchings, J. / Cheung, A.C.M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the complete, membrane-assembled COPII coat reveals a complex interaction network. Authors: Joshua Hutchings / Viktoriya G Stancheva / Nick R Brown / Alan C M Cheung / Elizabeth A Miller / Giulia Zanetti / ![]() ![]() Abstract: COPII mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Five essential proteins assemble into a two-layer architecture, with the inner layer thought to regulate coat ...COPII mediates Endoplasmic Reticulum to Golgi trafficking of thousands of cargoes. Five essential proteins assemble into a two-layer architecture, with the inner layer thought to regulate coat assembly and cargo recruitment, and the outer coat forming cages assumed to scaffold membrane curvature. Here we visualise the complete, membrane-assembled COPII coat by cryo-electron tomography and subtomogram averaging, revealing the full network of interactions within and between coat layers. We demonstrate the physiological importance of these interactions using genetic and biochemical approaches. Mutagenesis reveals that the inner coat alone can provide membrane remodelling function, with organisational input from the outer coat. These functional roles for the inner and outer coats significantly move away from the current paradigm, which posits membrane curvature derives primarily from the outer coat. We suggest these interactions collectively contribute to coat organisation and membrane curvature, providing a structural framework to understand regulatory mechanisms of COPII trafficking and secretion. | |||||||||
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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 | ![]() | 606.5 KB | Display | ![]() |
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PDB format | ![]() | 496.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 104 KB | Display | |
Data in CIF | ![]() | 156.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11199MC ![]() 6zg5C ![]() 6zg6C ![]() 6zl0C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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Components
-Protein transport protein ... , 2 types, 4 molecules AEBF
#1: Protein | Mass: 85332.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #2: Protein | Mass: 103733.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: SEC24, ANU1, YIL109C / Production host: ![]() ![]() |
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-Small COPII coat GTPase ... , 2 types, 2 molecules CG
#3: Protein | Mass: 21472.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P20606, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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#5: Protein | Mass: 21359.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() References: UniProt: P20606, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
-Protein/peptide , 1 types, 2 molecules DH
#4: Protein/peptide | Mass: 309.360 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() |
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-Non-polymers , 3 types, 8 molecules ![](data/chem/img/ZN.gif)
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#6: Chemical | ChemComp-ZN / #7: Chemical | #8: Chemical | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging |
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Sample preparation
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Buffer solution | pH: 6.8 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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 |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 3.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter slit width: 20 eV |
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Processing
Software | Name: PHENIX / Version: dev_3885: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Details: 3d ctf correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151176 / Symmetry type: POINT | ||||||||||||||||||||||||
EM volume selection | Num. of tomograms: 149 / Num. of volumes extracted: 800000 | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
Atomic model building |
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Refine LS restraints |
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