+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11194 | |||||||||
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Title | COPII on membranes, outer coat vertex | |||||||||
Map data | COPII on membranes - outer coat vertex | |||||||||
Sample |
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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 / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / 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 / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / 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 / intracellular protein transport / protein import into nucleus / nuclear envelope / endoplasmic reticulum membrane / structural molecule activity / positive regulation of DNA-templated transcription / endoplasmic reticulum Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | Zanetti G / Hutchings J | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nat Commun / Year: 2021 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. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11194.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-11194-v30.xml emd-11194.xml | 18.1 KB 18.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11194_fsc.xml | 6 KB | Display | FSC data file |
Images | emd_11194.png | 84.7 KB | ||
Masks | emd_11194_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-11194.cif.gz | 6.7 KB | ||
Others | emd_11194_half_map_1.map.gz emd_11194_half_map_2.map.gz | 4.2 MB 4.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11194 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11194 | HTTPS FTP |
-Validation report
Summary document | emd_11194_validation.pdf.gz | 789.7 KB | Display | EMDB validaton report |
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Full document | emd_11194_full_validation.pdf.gz | 789.3 KB | Display | |
Data in XML | emd_11194_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_11194_validation.cif.gz | 13.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11194 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11194 | HTTPS FTP |
-Related structure data
Related structure data | 6zg6MC 6zg5C 6zgaC 6zl0C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11194.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | COPII on membranes - outer coat vertex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.66 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11194_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11194_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11194_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : COPII coat assembled on lipid bilayer
Entire | Name: COPII coat assembled on lipid bilayer |
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Components |
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-Supramolecule #1: COPII coat assembled on lipid bilayer
Supramolecule | Name: COPII coat assembled on lipid bilayer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) |
-Macromolecule #1: Protein transport protein SEC31
Macromolecule | Name: Protein transport protein SEC31 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 138.833422 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVKLAEFSRT ATFAWSHDKI PLLVSGTVSG TVDANFSTDS SLELWSLLAA DSEKPIASLQ VDSKFNDLDW SHNNKIIAGA LDNGSLELY STNEANNAIN SMARFSNHSS SVKTVKFNAK QDNVLASGGN NGEIFIWDMN KCTESPSNYT PLTPGQSMSS V DEVISLAW ...String: MVKLAEFSRT ATFAWSHDKI PLLVSGTVSG TVDANFSTDS SLELWSLLAA DSEKPIASLQ VDSKFNDLDW SHNNKIIAGA LDNGSLELY STNEANNAIN SMARFSNHSS SVKTVKFNAK QDNVLASGGN NGEIFIWDMN KCTESPSNYT PLTPGQSMSS V DEVISLAW NQSLAHVFAS AGSSNFASIW DLKAKKEVIH LSYTSPNSGI KQQLSVVEWH PKNSTRVATA TGSDNDPSIL IW DLRNANT PLQTLNQGHQ KGILSLDWCH QDEHLLLSSG RDNTVLLWNP ESAEQLSQFP ARGNWCFKTK FAPEAPDLFA CAS FDNKIE VQTLQNLTNT LDEQETETKQ QESETDFWNN VSREESKEKP SVFHLQAPTW YGEPSPAAHW AFGGKLVQIT PDGK GVSIT NPKISGLESN TTLSEALKTK DFKPLINQRL VKVIDDVNEE DWNLLEKLSM DGTEEFLKEA LAFDNDESDA QDDAN NEKE DDGEEFFQQI ETNFQPEGDF SLSGNIEQTI SKNLVSGNIK SAVKNSLEND LLMEAMVIAL DSNNERLKES VKNAYF AKY GSKSSLSRIL YSISKREVDD LVENLDVSQW KFISKAIQNL YPNDIAQRNE MLIKLGDRLK ENGHRQDSLT LYLAAGS LD KVASIWLSEF PDLEDKLKKD NKTIYEAHSE CLTEFIERFT VFSNFINGSS TINNEQLIAK FLEFINLTTS TGNFELAT E FLNSLPSDNE EVKTEKARVL IASGKSLPAQ NPATATTSKA KYTNAKTNKN VPVLPTPGMP STTSIPSMQA PFYGMTPGA SANALPPKPY VPATTTSAPV HTEGKYAPPS QPSMASPFVN KTNSSTRLNS FAPPPNPYAT ATVPATNVST TSIPQNTFAP IQPGMPIMG DYNAQSSSIP SQPPINAVSG QTPHLNRKAN DGWNDLPLKV KEKPSRAKAV SVAPPNILST PTPLNGIPAN A ASTMPPPP LSRAPSSVSM VSPPPLHKNS RVPSLVATSE SPRASISNPY APPQSSQQFP IGTISTANQT SNTAQVASSN PY APPPQQR VATPLSGGVP PAPLPKASNP YAPTATTQPN GSSYPPTGPY TNNHTMTSPP PVFNKPPTGP PPISMKKRSN KLA SIEQNP SQGATYPPTL SSSASPLQPS QPPTLASQVN TSAENVSHEI PADQQPIVDF LKEELARVTP LTPKEYSKQL KDCD KRLKI LFYHLEKQDL LTQPTIDCLH DLVALMKEKK YKEAMVIHAN IATNHAQEGG NWLTGVKRLI GIAEATLN UniProtKB: Protein transport protein SEC31 |
-Macromolecule #2: Protein transport protein SEC13
Macromolecule | Name: Protein transport protein SEC13 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 33.082965 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA SSDGKVSVVE FKENGTTSPI IIDAHAIGVN SASWAPATIE E DGEHNGTK ...String: MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA SSDGKVSVVE FKENGTTSPI IIDAHAIGVN SASWAPATIE E DGEHNGTK ESRKFVTGGA DNLVKIWKYN SDAQTYVLES TLEGHSDWVR DVAWSPTVLL RSYLASVSQD RTCIIWTQDN EQ GPWKKTL LKEEKFPDVL WRASWSLSGN VLALSGGDNK VTLWKENLEG KWEPAGEVHQ UniProtKB: Protein transport protein SEC13 |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 424 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 6.8 |
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Grid | Details: C-FLAT GRIDS |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 3.5 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 3.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |