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- EMDB-11199: COPII on membranes, inner coat -

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Basic information

Entry
Database: EMDB / ID: EMD-11199
TitleCOPII on membranes, inner coat
Map dataCOPII assembled on membranes, inner coat, density modified
Sample
  • Complex: COPII coat assembled on membrane, inner coat
    • Complex: Protein transport protein SEC23
      • Protein or peptide: Protein transport protein SEC23
      • Protein or peptide: PRO-PRO-PRO
    • Complex: Protein transport protein SEC24
      • Protein or peptide: Protein transport protein SEC24
    • Complex: Small COPII coat GTPase SAR1
      • Protein or peptide: Small COPII coat GTPase SAR1
      • Protein or peptide: Small COPII coat GTPase SAR1
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
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 / nuclear envelope organization / COPII-mediated vesicle transport / vesicle organization / COPII-coated vesicle cargo loading / 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 / nuclear envelope organization / COPII-mediated vesicle transport / vesicle organization / COPII-coated vesicle cargo loading / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / signal sequence binding / mitochondrial fission / fungal-type vacuole membrane / mitochondrial membrane organization / reticulophagy / endoplasmic reticulum exit site / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / SNARE binding / macroautophagy / intracellular protein transport / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Golgi membrane / GTPase activity / endoplasmic reticulum membrane / GTP binding / endoplasmic reticulum / mitochondrion / zinc ion binding
Similarity search - Function
small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Protein transport protein Sec23 / Sec23, C-terminal / : / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich ...small GTPase SAR1 family profile. / Small GTPase superfamily, SAR1-type / Protein transport protein Sec23 / Sec23, C-terminal / : / Sec24-like, trunk domain / Zinc finger, Sec23/Sec24-type / Sec23/Sec24, trunk domain / Sec23/Sec24, helical domain / Sec23/Sec24 beta-sandwich / Zinc finger, Sec23/Sec24-type superfamily / Sec23/Sec24 helical domain superfamily / Sec23/Sec24 zinc finger / Sec23/Sec24 trunk domain / Sec23/Sec24 helical domain / Sec23/Sec24 beta-sandwich domain / Gelsolin-like domain superfamily / Gelsolin-like domain / Gelsolin repeat / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / ADF-H/Gelsolin-like domain superfamily / von Willebrand factor A-like domain superfamily / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein transport protein SEC23 / Small COPII coat GTPase SAR1 / Protein transport protein SEC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiaeaSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 4.6 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: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.08
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  • Surface view with fitted model
  • Atomic models: PDB-6zga
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6zga
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11199.png

Downloads & links

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Map

FileDownload / File: emd_11199.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOPII assembled on membranes, inner coat, density modified
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 196 pix.
= 260.092 Å		1.33 Å/pix.
x 196 pix.
= 260.092 Å		1.33 Å/pix.
x 196 pix.
= 260.092 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.327 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.74955904 - 1.0809355
Average (Standard dev.)2.3150136e-05 (±0.049129978)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 260.092 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3271.3271.327
M x/y/z196196196
origin x/y/z0.0000.0000.000
length x/y/z260.092260.092260.092
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS196196196
D min/max/mean-0.7501.0810.000

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Supplemental data

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Mask #1

Fileemd_11199_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: COPII assembled on membranes, inner coat, density modified...

Fileemd_11199_additional_1.map
AnnotationCOPII assembled on membranes, inner coat, density modified and sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11199_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11199_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 membrane, inner coat

EntireName: COPII coat assembled on membrane, inner coat
Components
  • Complex: COPII coat assembled on membrane, inner coat
    • Complex: Protein transport protein SEC23
      • Protein or peptide: Protein transport protein SEC23
      • Protein or peptide: PRO-PRO-PRO
    • Complex: Protein transport protein SEC24
      • Protein or peptide: Protein transport protein SEC24
    • Complex: Small COPII coat GTPase SAR1
      • Protein or peptide: Small COPII coat GTPase SAR1
      • Protein or peptide: Small COPII coat GTPase SAR1
  • Ligand: ZINC ION
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: COPII coat assembled on membrane, inner coat

SupramoleculeName: COPII coat assembled on membrane, inner coat / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: Protein transport protein SEC23

SupramoleculeName: Protein transport protein SEC23 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #3: Protein transport protein SEC24

SupramoleculeName: Protein transport protein SEC24 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Saccharomyces cerevisiaeaSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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Supramolecule #4: Small COPII coat GTPase SAR1

SupramoleculeName: Small COPII coat GTPase SAR1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3, #5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Protein transport protein SEC23

MacromoleculeName: Protein transport protein SEC23 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 85.332047 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DFETNEDING VRFTWNVFPS TRSDANSNVV PVGCLYTPLK EYDELNVAPY NPVVCSGPHC KSILNPYCVI DPRNSSWSCP ICNSRNHLP PQYTNLSQEN MPLELQSTTI EYITNKPVTV PPIFFFVVDL TSETENLDSL KESIITSLSL LPPNALIGLI T YGNVVQLH ...String:
DFETNEDING VRFTWNVFPS TRSDANSNVV PVGCLYTPLK EYDELNVAPY NPVVCSGPHC KSILNPYCVI DPRNSSWSCP ICNSRNHLP PQYTNLSQEN MPLELQSTTI EYITNKPVTV PPIFFFVVDL TSETENLDSL KESIITSLSL LPPNALIGLI T YGNVVQLH DLSSETIDRC NVFRGDREYQ LEALTEMLTG QKPTGPGGAA SHLPNAMNKV TPFSLNRFFL PLEQVEFKLN QL LENLSPD QWSVPAGHRP LRATGSALNI ASLLLQGCYK NIPARIILFA SGPGTVAPGL IVNSELKDPL RSHHDIDSDH AQH YKKACK FYNQIAQRVA ANGHTVDIFA GCYDQIGMSE MKQLTDSTGG VLLLTDAFST AIFKQSYLRL FAKDEEGYLK MAFN GNMAV KTSKDLKVQG LIGHASAVKK TDANNISESE IGIGATSTWK MASLSPYHSY AIFFEIANTA ANSNPMMSAP GSADR PHLA YTQFITTYQH SSGTNRIRVT TVANQLLPFG TPAIAASFDQ EAAAVLMARI AVHKAETDDG ADVIRWLDRT LIKLCQ KYA DYNKDDPQSF RLAPNFSLYP QFTYYLRRSQ FLSVFNNSPD ETAFYRHIFT REDTTNSLIM IQPTLTSFSM EDDPQPV LL DSISVKPNTI LLLDTFFFIL IYHGEQIAQW RKAGYQDDPQ YADFKALLEE PKLEAAELLV DRFPLPRFID TEAGGSQA R FLLSKLNPSD NYQDMARGGS TIVLTDDVSL QNFMTHLQQV AVSGQA

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Macromolecule #2: Protein transport protein SEC24

MacromoleculeName: Protein transport protein SEC24 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 103.73325 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSHHKKRVYP QAQLQYGQNA TPLQQPAQFM PPQDPAAAGM SYGQMGMPPQ GAVPSMGQQQ FLTPAQEQLH QQIDQATTSM NDMHLHNVP LVDPNAYMQP QVPVQMGTPL QQQQQPMAAP AYGQPSAAMG QNMRPMNQLY PIDLLTELPP PITDLTLPPP P LVIPPERM ...String:
MSHHKKRVYP QAQLQYGQNA TPLQQPAQFM PPQDPAAAGM SYGQMGMPPQ GAVPSMGQQQ FLTPAQEQLH QQIDQATTSM NDMHLHNVP LVDPNAYMQP QVPVQMGTPL QQQQQPMAAP AYGQPSAAMG QNMRPMNQLY PIDLLTELPP PITDLTLPPP P LVIPPERM LVPSELSNAS PDYIRSTLNA VPKNSSLLKK SKLPFGLVIR PYQHLYDDID PPPLNEDGLI VRCRRCRSYM NP FVTFIEQ GRRWRCNFCR LANDVPMQMD QSDPNDPKSR YDRNEIKCAV MEYMAPKEYT LRQPPPATYC FLIDVSQSSI KSG LLATTI NTLLQNLDSI PNHDERTRIS ILCVDNAIHY FKIPLDSENN EESADQINMM DIADLEEPFL PRPNSMVVSL KACR QNIET LLTKIPQIFQ SNLITNFALG PALKSAYHLI GGVGGKIIVV SGTLPNLGIG KLQRRNESGV VNTSKETAQL LSCQD SFYK NFTIDCSKVQ ITVDLFLASE DYMDVASLSN LSRFTAGQTH FYPGFSGKNP NDIVKFSTEF AKHISMDFCM ETVMRA RGS TGLRMSRFYG HFFNRSSDLC AFSTMPRDQS YLFEVNVDES IMADYCYVQV AVLLSLNNSQ RRIRIITLAM PTTESLA EV YASADQLAIA SFYNSKAVEK ALNSSLDDAR VLINKSVQDI LATYKKEIVV SNTAGGAPLR LCANLRMFPL LMHSLTKH M AFRSGIVPSD HRASALNNLE SLPLKYLIKN IYPDVYSLHD MADEAGLPVQ TEDGEATGTI VLPQPINATS SLFERYGLY LIDNGNELFL WMGGDAVPAL VFDVFGTQDI FDIPIGKQEI PVVENSEFNQ RVRNIINQLR NHDDVITYQS LYIVRGASLS EPVNHASAR EVATLRLWAS STLVEDKILN NESYREFLQI MKARISK

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Macromolecule #3: Small COPII coat GTPase SAR1

MacromoleculeName: Small COPII coat GTPase SAR1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.472564 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGWDIFGWF RDVLASLGLW NKHGKLLFLG LDNAGKTTLL HMLKNDRLAT LQPTWHPTSE ELAIGNIKFT TFDLGGHIQA RRLWKDYFP EVNGIVFLVD AADPERFDEA RVELDALFNI AELKDVPFVI LGNKIDAPNA VSEAELRSAL GLLNTTGSQR I EGQRPVEV FMCSVVMRNG YLEAFQWLSQ YI

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Macromolecule #4: PRO-PRO-PRO

MacromoleculeName: PRO-PRO-PRO / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 309.36 Da
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
PPP

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Macromolecule #5: Small COPII coat GTPase SAR1

MacromoleculeName: Small COPII coat GTPase SAR1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.359406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGWDIFGWF RDVLASLGLW NKHGKLLFLG LDNAGKTTLL HMLKNDRLAT LQPTWHPTSE ELAIGNIKFT TFDLGGHIQA RRLWKDYFP EVNGIVFLVD AADPERFDEA RVELDALFNI AELKDVPFVI LGNKIDAPNA VSEAELRSAL GLLNTTGSQR I EGQRPVEV FMCSVVMRNG YLEAFQWLSQ Y

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 7 / Number of copies: 2 / Formula: GNP
Molecular weightTheoretical: 522.196 Da
Chemical component information

ChemComp-GNP:
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GppNHp, GMPPNP, energy-carrying molecule analogue*YM

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 151176
ExtractionNumber tomograms: 149 / Number images used: 800000
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 model(PDB ID:

2qtv

,

1pcx

,

5kyw

)
RefinementProtocol: OTHER
Output model

PDB-6zga:
COPII on membranes, inner coat

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