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- PDB-6zg6: COPII on membranes, outer coat vertex -

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Basic information

Entry
Database: PDB / ID: 6zg6
TitleCOPII on membranes, outer coat vertex
Components
  • Protein transport protein SEC13
  • Protein transport protein SEC31
KeywordsPROTEIN TRANSPORT / SECRETION / TRAFFICKING
Function / homology
Function and homology information


positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / COPII-mediated vesicle transport / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum ...positive regulation of ER to Golgi vesicle-mediated transport / Seh1-associated complex / protein exit from endoplasmic reticulum / COPII-coated vesicle budding / nuclear pore localization / COPII-mediated vesicle transport / regulation of TORC1 signaling / COPII-coated vesicle cargo loading / nuclear pore outer ring / positive regulation of protein exit from endoplasmic reticulum / Transport of Mature mRNA derived from an Intron-Containing Transcript / COPII vesicle coat / Regulation of HSF1-mediated heat shock response / SUMOylation of SUMOylation proteins / mating projection tip / endoplasmic reticulum organization / SUMOylation of RNA binding proteins / SUMOylation of chromatin organization proteins / vacuolar membrane / nucleocytoplasmic transport / 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
Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / Sec13/Seh1 family / WD domain, G-beta repeat / WD40 repeat, conserved site ...Protein transport protein SEC31 / Protein transport protein SEC31 / Protein transport protein SEC31-like / SRA1/Sec31 / Steroid receptor RNA activator (SRA1) / Ancestral coatomer element 1, Sec16/Sec31 / Sec16 Sec23-binding domain / Sec13/Seh1 family / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Protein transport protein SEC31 / Protein transport protein SEC13
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 12 Å
AuthorsZanetti, G. / Hutchings, J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T002670/1 United Kingdom
European Research Council (ERC)852915 CRYTOCOP United Kingdom
CitationJournal: 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
DepositionJun 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _refine.ls_d_res_high

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Assembly

Deposited unit
A: Protein transport protein SEC31
B: Protein transport protein SEC13
C: Protein transport protein SEC31
D: Protein transport protein SEC13
E: Protein transport protein SEC31
F: Protein transport protein SEC13
G: Protein transport protein SEC31
H: Protein transport protein SEC13


Theoretical massNumber of molelcules
Total (without water)687,6668
Polymers687,6668
Non-polymers00
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Protein transport protein SEC31 / Protein WEB1


Mass: 138833.422 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC31, WEB1, YDL195W, D1229 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P38968
#2: Protein
Protein transport protein SEC13


Mass: 33082.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC13, ANU3, YLR208W, L8167.4 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q04491
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: COPII coat assembled on lipid bilayer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: C-FLAT GRIDS
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
113.5GATAN K2 SUMMIT (4k x 4k)
213.5GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
5NOVACTFCTF correction
8UCSF Chimeramodel fitting
12Dynamofinal Euler assignment
14Dynamo3D reconstruction
CTF correctionDetails: 3d ctf correction / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14099 / Num. of class averages: 1 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 149 / Num. of volumes extracted: 150000
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 2PM6

2pm6


Accession code: 2PM6 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 12 Å

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