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- EMDB-19416: COPII outer coat vertex from coated tubules -

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Basic information

Entry
Database: EMDB / ID: EMD-19416
TitleCOPII outer coat vertex from coated tubules
Map dataLocRes filtered consensus map.
Sample
  • Complex: COPII outer coat vertex in tubule arrangement
    • Protein or peptide: Sec31
    • Protein or peptide: Sec13
KeywordsCOPII / coat / PROTEIN TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 9.7 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: To Be Published
Title: Cryo-electron tomography reveals how COPII assembles on cargo-containing membranes
Authors: Zanetti G / Pyle E
History
DepositionJan 16, 2024-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19416.png

Downloads & links

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Map

FileDownload / File: emd_19416.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocRes filtered consensus map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.66 Å/pix.
x 128 pix.
= 340.224 Å		2.66 Å/pix.
x 128 pix.
= 340.224 Å		2.66 Å/pix.
x 128 pix.
= 340.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.658 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.2534302 - 0.6028526
Average (Standard dev.)-0.0000003957686 (±0.037912425)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 340.224 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19416_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_19416_half_map_1.map
AnnotationHalf map 1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_19416_half_map_2.map
AnnotationHalf map 2.
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 outer coat vertex in tubule arrangement

EntireName: COPII outer coat vertex in tubule arrangement
Components
  • Complex: COPII outer coat vertex in tubule arrangement
    • Protein or peptide: Sec31
    • Protein or peptide: Sec13

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Supramolecule #1: COPII outer coat vertex in tubule arrangement

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

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Macromolecule #4: Sec31

MacromoleculeName: Sec31 / type: protein_or_peptide / ID: 4 / 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 #5: Sec13

MacromoleculeName: Sec13 / type: protein_or_peptide / ID: 5 / 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
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 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: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number subtomograms used: 13529
ExtractionNumber tomograms: 326 / Number images used: 87500
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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