+Open data
-Basic information
Entry | Database: PDB / ID: 4bzk | ||||||
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Title | The structure of the COPII coat assembled on membranes | ||||||
Components |
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Keywords | PROTEIN TRANSPORT / SECRETION / TRAFFICKING | ||||||
Function / homology | Function and homology information Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / COPII-coated vesicle cargo loading / regulation of TORC1 signaling / nuclear pore outer ring / COPII vesicle coat ...Seh1-associated complex / positive regulation of ER to Golgi vesicle-mediated transport / protein exit from endoplasmic reticulum / COPII-mediated vesicle transport / COPII-coated vesicle budding / nuclear pore localization / COPII-coated vesicle cargo loading / regulation of TORC1 signaling / nuclear pore outer ring / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / mating projection tip / SUMOylation of RNA binding proteins / endoplasmic reticulum organization / SUMOylation of chromatin organization proteins / nucleocytoplasmic transport / vacuolar membrane / endoplasmic reticulum exit site / positive regulation of TOR signaling / mRNA transport / nuclear pore / ERAD pathway / positive regulation of TORC1 signaling / cell periphery / protein import into nucleus / nuclear envelope / protein transport / endoplasmic reticulum membrane / positive regulation of DNA-templated transcription / structural molecule activity / endoplasmic reticulum Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 40 Å | ||||||
Authors | Zanetti, G. / Prinz, S. / Daum, S. / Meister, A. / Schekman, R. / Bacia, K. / Briggs, J.A.G. | ||||||
Citation | Journal: Elife / Year: 2013 Title: The structure of the COPII transport-vesicle coat assembled on membranes. Authors: Giulia Zanetti / Simone Prinz / Sebastian Daum / Annette Meister / Randy Schekman / Kirsten Bacia / John A G Briggs / Abstract: Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, ...Coat protein complex II (COPII) mediates formation of the membrane vesicles that export newly synthesised proteins from the endoplasmic reticulum. The inner COPII proteins bind to cargo and membrane, linking them to the outer COPII components that form a cage around the vesicle. Regulated flexibility in coat architecture is essential for transport of a variety of differently sized cargoes, but structural data on the assembled coat has not been available. We have used cryo-electron tomography and subtomogram averaging to determine the structure of the complete, membrane-assembled COPII coat. We describe a novel arrangement of the outer coat and find that the inner coat can assemble into regular lattices. The data reveal how coat subunits interact with one another and with the membrane, suggesting how coordinated assembly of inner and outer coats can mediate and regulate packaging of vesicles ranging from small spheres to large tubular carriers. DOI:http://dx.doi.org/10.7554/eLife.00951.001. | ||||||
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 | 4bzk.cif.gz | 412.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bzk.ent.gz | 318 KB | Display | PDB format |
PDBx/mmJSON format | 4bzk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bzk_validation.pdf.gz | 768.5 KB | Display | wwPDB validaton report |
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Full document | 4bzk_full_validation.pdf.gz | 911.8 KB | Display | |
Data in XML | 4bzk_validation.xml.gz | 70.9 KB | Display | |
Data in CIF | 4bzk_validation.cif.gz | 104.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/4bzk ftp://data.pdbj.org/pub/pdb/validation_reports/bz/4bzk | HTTPS FTP |
-Related structure data
Related structure data | 2431MC 2428C 2429C 2430C 2432C 4bziC 4bzjC 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: Protein | Mass: 138833.422 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC31, WEB1, YDL195W, D1229 / Plasmid: PNS3141 (6H31/CK1313) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY1112 / References: UniProt: P38968 #2: Protein | | Mass: 33082.965 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC13, ANU3, YLR208W, L8167.4 / Plasmid: PNS3141 (6H31/CK1313) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY1112 / References: UniProt: Q04491 #3: Protein | | Mass: 33191.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SEC13, ANU3, YLR208W, L8167.4 / Plasmid: PNS3141 (6H31/CK1313) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY1112 / References: UniProt: Q04491 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: SEC13/31 COMPLEX (AS PART OF COMPLETE COPII ASSEMBLED ON MEMBRANE) EDGE IN LEFT-HANDED DIRECTION Type: COMPLEX |
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Buffer solution | Name: HEPES, 50 MM KOAC, 1.2 MM MGCL2 / pH: 6.8 / Details: HEPES, 50 MM KOAC, 1.2 MM MGCL2 |
Specimen | Conc.: 0.03 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: C-FLAT GRIDS / Grid type: C-flat |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: ETHANE; HOMEMADE PLUNGER |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Sep 18, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 19500 X / Nominal defocus max: 3200 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Specimen holder | Tilt angle max: 60 ° / Tilt angle min: -60 ° |
Image recording | Electron dose: 80 e/Å2 / Film or detector model: GATAN MULTISCAN |
Image scans | Num. digital images: 26 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH TILTED IMAGE WITHIN TOMOGRAM | |||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||
3D reconstruction | Method: SUBTOMOGRAM ALIGNMENT AND AVERAGING / Resolution: 40 Å / Num. of particles: 192 / Nominal pixel size: 4.3 Å / Actual pixel size: 4.3 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2431. (DEPOSITION ID: 11863). Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | |||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 40 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 40 Å
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