+Open data
-Basic information
Entry | Database: PDB / ID: 4bzi | ||||||
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Title | The structure of the COPII coat assembled on membranes | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / SECRETION / TRAFFICKING / SEC23 / SEC24 / SAR1 | ||||||
Function / homology | Function and homology information 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 / signal sequence binding / mitochondrial fission / 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 / Golgi apparatus / endoplasmic reticulum / mitochondrion / zinc ion binding Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 23 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 | 4bzi.cif.gz | 1017.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bzi.ent.gz | 789.9 KB | Display | PDB format |
PDBx/mmJSON format | 4bzi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bzi_validation.pdf.gz | 975.8 KB | Display | wwPDB validaton report |
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Full document | 4bzi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4bzi_validation.xml.gz | 136.1 KB | Display | |
Data in CIF | 4bzi_validation.cif.gz | 206.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/4bzi ftp://data.pdbj.org/pub/pdb/validation_reports/bz/4bzi | HTTPS FTP |
-Related structure data
Related structure data | 2428MC 2429C 2430C 2431C 2432C 4bzjC 4bzkC 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
-Protein , 4 types, 12 molecules ADGBJKELMFNO
#1: Protein | Mass: 85463.242 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PTKY9 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY3764 / References: UniProt: E7QAP0, UniProt: P15303*PLUS #2: Protein | Mass: 21472.564 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PTY40 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): KBB1012 / References: UniProt: C8ZIG2, UniProt: P20606*PLUS #3: Protein | Mass: 103733.250 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PTKY9 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY3764 / References: UniProt: C8ZAD6, UniProt: P40482*PLUS #4: Protein | Mass: 103675.172 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Plasmid: PTKY9 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): RSY3764 / References: UniProt: C8ZAD6, UniProt: P40482*PLUS |
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-Non-polymers , 3 types, 12 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | #7: Chemical | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: electron tomography |
-Sample preparation
Component | Name: SEC23-23-SAR1 / Type: COMPLEX |
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Buffer solution | Name: MM HEPES, 50 MM KOAC, 1.2 MM MGCL2 / pH: 6.8 / Details: MM 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: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-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 |
-Processing
EM software |
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CTF correction | Details: EACH TILTED IMAGE WITHIN TOMOGRAM | |||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Method: SUBTOMOGRAM ALIGNMENT AND AVERAGING / Resolution: 23 Å / Num. of particles: 15000 / Actual pixel size: 4.3 Å Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2428. (DEPOSITION ID: 11856). 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 | PDB-ID: 1M2O Accession code: 1M2O / Source name: PDB / Type: experimental model | |||||||||||||||
Refinement | Highest resolution: 23 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 23 Å
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