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- EMDB-11197: COPII assembled on membranes, outer coat right-handed rod, class 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-11197
TitleCOPII assembled on membranes, outer coat right-handed rod, class 2
Map dataouter COPII coat on membranes, right-hended rods with extra rod
Sample
  • Complex: COPII coat assembled on lipid bilayer
    • Protein or peptide: Sec31
    • Protein or peptide: Sec13
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
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 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...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 / Sec23-binding domain of Sec16 / Sec13/Seh1 family / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / 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 (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae S288C (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsZanetti G / Hutchings J
Funding support United Kingdom, 2 items
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, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11197.png

Downloads & links

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Map

FileDownload / File: emd_11197.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationouter COPII coat on membranes, right-hended rods with extra rod
Voxel sizeX=Y=Z: 2.66 Å
Density
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-4.2138257 - 10.726866
Average (Standard dev.)3.222118e-11 (±1.1710383)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.662.662.66
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z340.480340.480340.480
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-4.21410.7270.000

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Supplemental data

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Mask #1

Fileemd_11197_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11197_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11197_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : COPII coat assembled on lipid bilayer

EntireName: COPII coat assembled on lipid bilayer
Components
  • Complex: COPII coat assembled on lipid bilayer
    • Protein or peptide: Sec31
    • Protein or peptide: Sec13

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Supramolecule #1: COPII coat assembled on lipid bilayer

SupramoleculeName: COPII coat assembled on lipid bilayer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Macromolecule #1: Sec31

MacromoleculeName: Sec31 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MVKLAEFSRT ATFAWSHDKI PLLVSGTVSG TVDANFSTDS SLELWSLLAA DSEKPIASLQ VDSKFNDLD WSHNNKIIAG ALDNGSLELY STNEANNAIN SMARFSNHSS SVKTVKFNAK Q DNVLASGG NNGEIFIWDM NKCTESPSNY TPLTPGQSMS SVDEVISLAW ...String:
MVKLAEFSRT ATFAWSHDKI PLLVSGTVSG TVDANFSTDS SLELWSLLAA DSEKPIASLQ VDSKFNDLD WSHNNKIIAG ALDNGSLELY STNEANNAIN SMARFSNHSS SVKTVKFNAK Q DNVLASGG NNGEIFIWDM NKCTESPSNY TPLTPGQSMS SVDEVISLAW NQSLAHVFAS AG SSNFASI WDLKAKKEVI HLSYTSPNSG IKQQLSVVEW HPKNSTRVAT ATGSDNDPSI LIW DLRNAN TPLQTLNQGH QKGILSLDWC HQDEHLLLSS GRDNTVLLWN PESAEQLSQF PARG NWCFK TKFAPEAPDL FACASFDNKI EVQTLQNLTN TLDEQETETK QQESETDFWN NVSRE ESKE KPTVFHLQAP TWYGEPSPAA HWAFGGKLVQ ITPDGKGVSI TNPKISGLES NTTLSE ALK TKDFKPLINQ RLVKVIDDVN EEDWNLLEKL SMDGTEEFLK EALAFDNDES DAQDDAN NE KEDDGEEFFQ QIETNFQPEG DFSLSGNIEQ TISKNLVSGN IKSAVKNSLE NDLLMEAM V IALDSNNERL KESVKNAYFA KYGSKSSLSR ILYSISKREV DDLVENLDVS QWKFISKAI QNLYPNDIAQ RNEMLIKLGD RLKENGHRQD SLTLYLAAGS LDKVASIWLS EFPDLEDKLK KDNKTIYEA HSECLTEFIE RFTVFSNFIN GSSTINNEQL IAKFLEFINL TTSTGNFELA T EFLNSLPS DNEEVKTEKA RVLIASGKSL PAQNPATATT SKAKYTNAKT NKNVPVLPTP GM PSTTSIP SMQAPFYGMT PGASANALPP KPYVPATTTS APVHTEGKYA PPSQPSMASP FVN KTNSST RLNSFAPPPN PYATATVPAT NVSTTSIPQN TFAPIQPGMP IMGDYNAQSS SIPS QPPIN AVSGQTPHLN RKANDGWNDL PLKVKEKPSR AKAVSVAPPN ILSTPTPLNG IPANA ASTM PPPPLSRAPS SVSMVSPPPL HKNSRVPSLV ATSESPRASI SNPYAPPQSS QQFPIG TIS TANQTSNTAQ VASSNPYAPP PQQRVATPLS GGVPPAPLPK ASNPYAPTAT TQPNGSS YP PTGPYTNNHT MTSPPPVFNK PPTGPPPISM KKRSNKLASI EQNPSQGATY PPTLSSSA S PLQPSQPPTL ASQVNTSAEN VSHEIPADQQ PIVDFLKEEL ARVTPLTPKE YSKQLKDCD KRLKILFYHL EKQDLLTQPT IDCLHDLVAL MKEKKYKEAM VIHANIATNH AQEGGNWLTG VKRLIGIAE ATLN

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Macromolecule #2: Sec13

MacromoleculeName: Sec13 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
SequenceString: MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTI LASCSYDGKV LIWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA S SDGKVSVV EFKENGTTSP IIIDAHAIGV NSASWAPATI EEDGEHNGTK ...String:
MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT GHEGPVWRVD WAHPKFGTI LASCSYDGKV LIWKEENGRW SQIAVHAVHS ASVNSVQWAP HEYGPLLLVA S SDGKVSVV EFKENGTTSP IIIDAHAIGV NSASWAPATI EEDGEHNGTK ESRKFVTGGA DN LVKIWKY NSDAQTYVLE STLEGHSDWV RDVAWSPTVL LRSYLASVSQ DRTCIIWTQD NEQ GPWKKT LLKEEKFPDV LWRASWSLSG NVLALSGGDN KVTLWKENLE GKWEPAGEVH Q

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 7195
ExtractionNumber tomograms: 149 / Number images used: 150000
CTF correctionSoftware: (Name: CTFFIND, NOVACTF) / Details: 3d ctf correction
Final angle assignmentType: NOT APPLICABLE / Software - Name: Dynamo
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2pm6

RefinementProtocol: RIGID BODY FIT

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