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- EMDB-19418: COPII outer coat vertex on vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-19418
TitleCOPII outer coat vertex on vesicles
Map dataMap.
Sample
  • Complex: COPII outer coat vertex on vesicles
    • Protein or peptide: Sec31
    • Protein or peptide: Sec13
KeywordsCOPII / coat / PROTEIN TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 11.4 Å
AuthorsZanetti G / Pyle E
Funding supportEuropean Union, United Kingdom, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)852915European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T002670/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes.
Authors: Euan Pyle / Elizabeth A Miller / Giulia Zanetti /
Abstract: Proteins traverse the eukaryotic secretory pathway through membrane trafficking between organelles. The coat protein complex II (COPII) mediates the anterograde transport of newly synthesized ...Proteins traverse the eukaryotic secretory pathway through membrane trafficking between organelles. The coat protein complex II (COPII) mediates the anterograde transport of newly synthesized proteins from the endoplasmic reticulum, engaging cargoes with a wide range of size and biophysical properties. The native architecture of the COPII coat and how cargo might influence COPII carrier morphology remain poorly understood. Here we reconstituted COPII-coated membrane carriers using purified Saccharomyces cerevisiae proteins and cell-derived microsomes as a native membrane source. Using cryo-electron tomography with subtomogram averaging, we demonstrate that the COPII coat binds cargo and forms largely spherical vesicles from native membranes. We reveal the architecture of the inner and outer coat layers and shed light on how spherical carriers are formed. Our results provide insights into the architecture and regulation of the COPII coat and advance our current understanding of how membrane curvature is generated.
History
DepositionJan 16, 2024-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19418.png

Downloads & links

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Map

FileDownload / File: emd_19418.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.05 Å/pix.
x 128 pix.
= 390.656 Å		3.05 Å/pix.
x 128 pix.
= 390.656 Å		3.05 Å/pix.
x 128 pix.
= 390.656 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.18801837 - 0.2768329
Average (Standard dev.)0.00081891514 (±0.016765323)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 390.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19418_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_19418_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_19418_half_map_2.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : COPII outer coat vertex on vesicles

EntireName: COPII outer coat vertex on vesicles
Components
  • Complex: COPII outer coat vertex on vesicles
    • Protein or peptide: Sec31
    • Protein or peptide: Sec13

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Supramolecule #1: COPII outer coat vertex on vesicles

SupramoleculeName: COPII outer coat vertex on vesicles / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: COPII outer coat vertex on vesicles
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 171 KDa

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Macromolecule #1: Sec31

MacromoleculeName: Sec31 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVKLAEFSRT ATFAWSHDK I PLLVSGTV SG TVDANFS TDS SLELWS LLAA DSEKP IASLQ VDSK FNDLDW SHN NKIIAGA LD NGSLELYS T NEANNAINS MARFSNHSSS VKTVKFNAK Q DNVLASGG NN GEIFIWD MNK CTESPS NYTP LTPGQ ...String:
MVKLAEFSRT ATFAWSHDK I PLLVSGTV SG TVDANFS TDS SLELWS LLAA DSEKP IASLQ VDSK FNDLDW SHN NKIIAGA LD NGSLELYS T NEANNAINS MARFSNHSSS VKTVKFNAK Q DNVLASGG NN GEIFIWD MNK CTESPS NYTP LTPGQ SMSSV DEVI SLAWNQ SLA HVFASAG SS NFASIWDL K AKKEVIHLS YTSPNSGIKQ QLSVVEWHP K NSTRVATA TG SDNDPSI LIW DLRNAN TPLQ TLNQG HQKGI LSLD WCHQDE HLL LSSGRDN TV LLWNPESA E QLSQFPARG NWCFKTKFAP EAPDLFACA S FDNKIEVQ TL QNLTNTL DEQ ETETKQ QESE TDFWN NVSRE ESKE KPSVFH LQA PTWYGEP SP AAHWAFGG K LVQITPDGK GVSITNPKIS GLESNTTLS E ALKTKDFK PL INQRLVK VID DVNEED WNLL EKLSM DGTEE FLKE ALAFDN DES DAQDDAN NE KEDDGEEF F QQIETNFQP EGDFSLSGNI EQTISKNLV S GNIKSAVK NS LENDLLM EAM VIALDS NNER LKESV KNAYF AKYG SKSSLS RIL YSISKRE VD DLVENLDV S QWKFISKAI QNLYPNDIAQ RNEMLIKLG D RLKENGHR QD SLTLYLA AGS LDKVAS IWLS EFPDL EDKLK KDNK TIYEAH SEC LTEFIER FT VFSNFING S STINNEQLI AKFLEFINLT TSTGNFELA T EFLNSLPS DN EEVKTEK ARV LIASGK SLPA QNPAT ATTSK AKYT NAKTNK NVP VLPTPGM PS TTSIPSMQ A PFYGMTPGA SANALPPKPY VPATTTSAP V HTEGKYAP PS QPSMASP FVN KTNSST RLNS FAPPP NPYAT ATVP ATNVST TSI PQNTFAP IQ PGMPIMGD Y NAQSSSIPS QPPINAVSGQ TPHLNRKAN D GWNDLPLK VK EKPSRAK AVS VAPPNI LSTP TPLNG IPANA ASTM PPPPLS RAP SSVSMVS PP PLHKNSRV P SLVATSESP RASISNPYAP PQSSQQFPI G TISTANQT SN TAQVASS NPY APPPQQ RVAT PLSGG VPPAP LPKA SNPYAP TAT TQPNGSS YP PTGPYTNN H TMTSPPPVF NKPPTGPPPI SMKKRSNKL A SIEQNPSQ GA TYPPTLS SSA SPLQPS QPPT LASQV NTSAE NVSH EIPADQ QPI VDFLKEE LA RVTPLTPK E YSKQLKDCD KRLKILFYHL EKQDLLTQP T IDCLHDLV AL MKEKKYK EAM VIHANI ATNH AQEGG NWLTG VKRL IGIAEA TLN

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Macromolecule #2: Sec13

MacromoleculeName: Sec13 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVVIANAHNE LIHDAVLDY Y GKRLATCS SD KTIKIFE VEG ETHKLI DTLT GHEGP VWRVD WAHP KFGTIL ASC SYDGKVL IW KEENGRWS Q IAVHAVHSA SVNSVQWAPH EYGPLLLVA S SDGKVSVV EF KENGTTS PII IDAHAI GVNS ASWAP ...String:
MVVIANAHNE LIHDAVLDY Y GKRLATCS SD KTIKIFE VEG ETHKLI DTLT GHEGP VWRVD WAHP KFGTIL ASC SYDGKVL IW KEENGRWS Q IAVHAVHSA SVNSVQWAPH EYGPLLLVA S SDGKVSVV EF KENGTTS PII IDAHAI GVNS ASWAP ATIEE DGEH NGTKES RKF VTGGADN LV KIWKYNSD A QTYVLESTL EGHSDWVRDV AWSPTVLLR S YLASVSQD RT CIIWTQD NEQ GPWKKT LLKE EKFPD VLWRA SWSL SGNVLA LSG GDNKVTL WK ENLEGKWE P AGEVHQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Software - details: Alpha version / Number subtomograms used: 19368
ExtractionNumber tomograms: 765 / Number images used: 23932
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5) / Software - details: Alpha version
FSC plot (resolution estimation)

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