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- EMDB-11264: COPII on membranes, outer coat left-handed rod -

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Basic information

Entry
Database: EMDB / ID: EMD-11264
TitleCOPII on membranes, outer coat left-handed rod
Map dataCOPII assembled on membranes, outer coat, left handed rod
Sample
  • Complex: COPII coat assembled on lipid bilayer
    • Protein or peptide: Protein transport protein SEC31
    • Protein or peptide: Protein transport protein SEC13
KeywordsPROTEIN 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-coated vesicle budding / COPII-mediated vesicle transport / 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-coated vesicle budding / COPII-mediated vesicle transport / 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 / protein transport / nuclear envelope / 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 / 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)
Methodsubtomogram averaging / cryo EM / Resolution: 40.0 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 30, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6zl0
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zl0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11264.png

Downloads & links

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Map

FileDownload / File: emd_11264.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOPII assembled on membranes, outer coat, left handed rod
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 128 pix.
= 340.48 Å		2.66 Å/pix.
x 128 pix.
= 340.48 Å		2.66 Å/pix.
x 128 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0 / Movie #1: 5
Minimum - Maximum-6.219357 - 14.818194999999999
Average (Standard dev.)-0.000000000724255 (±1.3305035)
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-6.21914.818-0.000

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Supplemental data

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Mask #1

Fileemd_11264_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11264_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_11264_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: Protein transport protein SEC31
    • Protein or peptide: Protein transport protein 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)

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Macromolecule #1: Protein transport protein SEC31

MacromoleculeName: Protein transport protein SEC31 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 138.847438 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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 TVFHLQAPTW 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

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Macromolecule #2: Protein transport protein SEC13

MacromoleculeName: Protein transport protein SEC13 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 33.082965 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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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
GridDetails: C-FLAT GRIDS
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 40.0 Å / Software - Name: Dynamo
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD -2430. (DEPOSITION ID: 11862).
Number subtomograms used: 182
ExtractionNumber tomograms: 149 / Number images used: 150000
Final angle assignmentType: NOT APPLICABLE / Software - Name: Dynamo
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2pm6


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6zl0:
COPII on membranes, outer coat left-handed rod

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