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- EMDB-19417: COPII inner coat on vesicles -

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Basic information

Entry
Database: EMDB / ID: EMD-19417
TitleCOPII inner coat on vesicles
Map dataMap.
Sample
  • Complex: COPII inner coat on vesicles
    • Protein or peptide: Sec24
    • Protein or peptide: Sec23
    • Protein or peptide: Sar1
KeywordsCOPII / coat / PROTEIN TRANSPORT
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 14.4 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: 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_19417.png

Downloads & links

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Map

FileDownload / File: emd_19417.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: 0.0863
Minimum - Maximum-0.06062308 - 0.18542963
Average (Standard dev.)0.0077098534 (±0.024778109)
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_19417_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2.

Fileemd_19417_half_map_1.map
AnnotationHalf map 2.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1.

Fileemd_19417_half_map_2.map
AnnotationHalf map 1.
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 inner coat on vesicles

EntireName: COPII inner coat on vesicles
Components
  • Complex: COPII inner coat on vesicles
    • Protein or peptide: Sec24
    • Protein or peptide: Sec23
    • Protein or peptide: Sar1

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Supramolecule #1: COPII inner coat on vesicles

SupramoleculeName: COPII inner coat on vesicles / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: COPII inner coat on vesicles formed from native-like membranes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 210 KDa

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Macromolecule #1: Sec24

MacromoleculeName: Sec24 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSHHKKRVYP QAQLQYGQN A TPLQQPAQ FM PPQDPAA AGM SYGQMG MPPQ GAVPS MGQQQ FLTP AQEQLH QQI DQATTSM ND MHLHNVPL V DPNAYMQPQ VPVQMGTPLQ QQQQPMAAP A YGQPSAAM GQ NMRPMNQ LYP IDLLTE LPPP ITDLT ...String:
MSHHKKRVYP QAQLQYGQN A TPLQQPAQ FM PPQDPAA AGM SYGQMG MPPQ GAVPS MGQQQ FLTP AQEQLH QQI DQATTSM ND MHLHNVPL V DPNAYMQPQ VPVQMGTPLQ QQQQPMAAP A YGQPSAAM GQ NMRPMNQ LYP IDLLTE LPPP ITDLT LPPPP LVIP PERMLV PSE LSNASPD YI RSTLNAVP K NSSLLKKSK LPFGLVIRPY QHLYDDIDP P PLNEDGLI VR CRRCRSY MNP FVTFIE QGRR WRCNF CRLAN DVPM QMDQSD PND PKSRYDR NE IKCAVMEY M APKEYTLRQ PPPATYCFLI DVSQSSIKS G LLATTINT LL QNLDSIP NHD ERTRIS ILCV DNAIH YFKIP LDSE NNEESA DQI NMMDIAD LE EPFLPRPN S MVVSLKACR QNIETLLTKI PQIFQSNLI T NFALGPAL KS AYHLIGG VGG KIIVVS GTLP NLGIG KLQRR NESG VVNTSK ETA QLLSCQD SF YKNFTIDC S KVQITVDLF LASEDYMDVA SLSNLSRFT A GQTHFYPG FS GKNPNDI VKF STEFAK HISM DFCME TVMRA RGST GLRMSR FYG HFFNRSS DL CAFSTMPR D QSYLFEVNV DESIMADYCY VQVAVLLSL N NSQRRIRI IT LAMPTTE SLA EVYASA DQLA IASFY NSKAV EKAL NSSLDD ARV LINKSVQ DI LATYKKEI V VSNTAGGAP LRLCANLRMF PLLMHSLTK H MAFRSGIV PS DHRASAL NNL ESLPLK YLIK NIYPD VYSLH DMAD EAGLPV QTE DGEATGT IV LPQPINAT S SLFERYGLY LIDNGNELFL WMGGDAVPA L VFDVFGTQ DI FDIPIGK QEI PVVENS EFNQ RVRNI INQLR NHDD VITYQS LYI VRGASLS EP VNHASARE V ATLRLWASS TLVEDKILNN ESYREFLQI M KARISK

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Macromolecule #2: Sec23

MacromoleculeName: Sec23 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DFETNEDING VRFTWNVFP S TRSDANSN VV PVGCLYT PLK EYDELN VAPY NPVVC SGPHC KSIL NPYCVI DPR NSSWSCP IC NSRNHLPP Q YTNLSQENM PLELQSTTIE YITNKPVTV P PIFFFVVD LT SETENLD SLK ESIITS LSLL PPNAL ...String:
DFETNEDING VRFTWNVFP S TRSDANSN VV PVGCLYT PLK EYDELN VAPY NPVVC SGPHC KSIL NPYCVI DPR NSSWSCP IC NSRNHLPP Q YTNLSQENM PLELQSTTIE YITNKPVTV P PIFFFVVD LT SETENLD SLK ESIITS LSLL PPNAL IGLIT YGNV VQLHDL SSE TIDRCNV FR GDREYQLE A LTEMLTGQK PTGPGGAASH LPNAMNKVT P FSLNRFFL PL EQVEFKL NQL LENLSP DQWS VPAGH RPLRA TGSA LNIASL LLQ GCYKNIP AR IILFASGP G TVAPGLIVN SELKDPLRSH HDIDSDHAQ H YKKACKFY NQ IAQRVAA NGH TVDIFA GCYD QIGMS EMKQL TDST GGVLLL TDA FSTAIFK QS YLRLFAKD E EGYLKMAFN GNMAVKTSKD LKVQGLIGH A SAVKKTDA NN ISESEIG IGA TSTWKM ASLS PYHSY AIFFE IANT AANSNP MMS APGSADR PH LAYTQFIT T YQHSSGTNR IRVTTVANQL LPFGTPAIA A SFDQEAAA VL MARIAVH KAE TDDGAD VIRW LDRTL IKLCQ KYAD YNKDDP QSF RLAPNFS LY PQFTYYLR R SQFLSVFNN SPDETAFYRH IFTREDTTN S LIMIQPTL TS FSMEDDP QPV LLDSIS VKPN TILLL DTFFF ILIY HGEQIA QWR KAGYQDD PQ YADFKALL E EPKLEAAEL LVDRFPLPRF IDTEAGGSQ A RFLLSKLN PS DNYQDMA RGG STIVLT DDVS LQNFM THLQQ VAVS GQA

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Macromolecule #3: Sar1

MacromoleculeName: Sar1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGWDIFGWF RDVLASLGL W NKHGKLLF LG LDNAGKT TLL HMLKND RLAT LQPTW HPTSE ELAI GNIKFT TFD LGGHIQA RR LWKDYFPE V NGIVFLVDA ADPERFDEAR VELDALFNI A ELKDVPFV IL GNKIDAP NAV SEAELR SALG LLNTT ...String:
MAGWDIFGWF RDVLASLGL W NKHGKLLF LG LDNAGKT TLL HMLKND RLAT LQPTW HPTSE ELAI GNIKFT TFD LGGHIQA RR LWKDYFPE V NGIVFLVDA ADPERFDEAR VELDALFNI A ELKDVPFV IL GNKIDAP NAV SEAELR SALG LLNTT GSQRI EGQR PVEVFM CSV VMRNGYL EA FQWLSQYI

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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
GridModel: EMS Lacey Carbon / Material: COPPER / Pretreatment - Type: PLASMA CLEANING
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Software - details: Alpha version / Number subtomograms used: 12187
ExtractionNumber tomograms: 765 / Number images used: 13248
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5) / Software - details: Alpha version
FSC plot (resolution estimation)

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