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- EMDB-15949: COPII inner coat reprocessed with relion4.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-15949
TitleCOPII inner coat reprocessed with relion4.0
Map dataCOPII inner coat
Sample
  • Complex: COPII coat assembled on membrane, inner coat
    • Complex: Protein transport protein SEC23Protein targeting
      • Protein or peptide: inner COPII coat complex
    • Complex: Protein transport protein SEC24Protein targeting
    • Complex: Small COPII coat GTPase SAR1
KeywordsCOPII / Sec23 Sec24 Sar1 / PROTEIN TRANSPORT
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 / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear envelope organization / vesicle organization / 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 / COPII-coated vesicle budding / COPII-mediated vesicle transport / nuclear envelope organization / vesicle organization / COPII vesicle coat / positive regulation of protein exit from endoplasmic reticulum / membrane organization / mitochondrial fission / mitochondrial membrane organization / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum exit site / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum membrane / Golgi apparatus / 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 / Zinc finger, Sec23/Sec24-type superfamily ...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 / Sar1p-like members of the Ras-family of small GTPases / Gelsolin-like domain / Gelsolin repeat / 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
SEC24 isoform 1 / Protein transport protein SEC23 / Small COPII coat GTPase SAR1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiaeaSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsubtomogram averaging / cryo EM / Resolution: 3.8 Å
AuthorsZanetti G / Pyle E
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)852915European Union
Citation
Journal: Elife / Year: 2022
Title: A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0.
Authors: Jasenko Zivanov / Joaquín Otón / Zunlong Ke / Andriko von Kügelgen / Euan Pyle / Kun Qu / Dustin Morado / Daniel Castaño-Díez / Giulia Zanetti / Tanmay A M Bharat / John A G Briggs / Sjors H W Scheres /
Abstract: We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are ...We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope. Implementation of our approaches in the open-source software package RELION aims to facilitate their general use, particularly for those researchers who are already familiar with its single-particle analysis tools. We illustrate for three applications that our approaches allow structure determination from cryo-ET data to resolutions sufficient for de novo atomic modelling.
#1: Journal: Biorxiv / Year: 2022
Title: A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0
Authors: Zivanov J / Oton J / Ke Z / von Kugelgen A / Pyle E / Qu K / Morado D / Castano-Diez D / Zanetti G / Bharat TAM / Briggs JAG / Scheres SHW
History
DepositionOct 11, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15949.png

Downloads & links

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Map

FileDownload / File: emd_15949.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCOPII inner coat
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 196 pix.
= 254.8 Å		1.3 Å/pix.
x 196 pix.
= 254.8 Å		1.3 Å/pix.
x 196 pix.
= 254.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 17.0
Minimum - Maximum-55.158470000000001 - 91.151115000000004
Average (Standard dev.)0.000010426426 (±3.5622861)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 254.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15949_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half2

Fileemd_15949_half_map_1.map
Annotationhalf2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half1

Fileemd_15949_half_map_2.map
Annotationhalf1
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 SEC23Protein targeting
      • Protein or peptide: inner COPII coat complex
    • Complex: Protein transport protein SEC24Protein targeting
    • Complex: Small COPII coat GTPase SAR1

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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-#5

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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)

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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)

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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)

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Macromolecule #1: inner COPII coat complex

MacromoleculeName: inner COPII coat complex / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Spodoptera (butterflies/moths)
SequenceString: DFETNEDING VRFTWNVFPS TRSDANSNVV PVGCLYTPLK EYDELNVAPY NPVVCSGPHC KSILNPYCVI DPRNSSWSCP ICNSRNHLPP QYTNLSQENM PLELQSTTIE YITNKPVTVP PIFFFVVDLT SETENLDSLK ESIITSLSLL PPNALIGLIT YGNVVQLHDL ...String:
DFETNEDING VRFTWNVFPS TRSDANSNVV PVGCLYTPLK EYDELNVAPY NPVVCSGPHC KSILNPYCVI DPRNSSWSCP ICNSRNHLPP QYTNLSQENM PLELQSTTIE YITNKPVTVP PIFFFVVDLT SETENLDSLK ESIITSLSLL PPNALIGLIT YGNVVQLHDL SSETIDRCNV FRGDREYQLE ALTEMLTGQK PTGPGGAASH LPNAMNKVTP FSLNRFFLP LEQVEFKLNQ LLENLSPDQW SVPAGHRPLR ATGSALNIAS LLLQGCYKNI PARIILFASG PGTVAPGLIV NSELKDPLRS HHDIDSDHAQ HYKKACKFYN QIAQRVAANG HTVDIFAGCY DQIGMSEMKQ LTDSTGGVLL LTDAFSTAIF KQSYLRLFAK DEEGYLKMAF NGNMAVKTSK DLKVQGLIGH ASAVKKTDAN NISESEIGIG A TSTWKMAS LSPYHSYAIF FEIANTAANS NPMMSAPGSA DRPHLAYTQF ITTYQHSSGT NRIRVTTVAN QLLPFGTPAI AASFDQEAAA VLMARIAVHK AETDDGADVI RWLDRTLIKL CQKYADYNKD DPQSFRLAPN FSLYPQFTYY LRRSQFLSVF NNSPDETAFY RHIFTREDTT NSLIMIQPTL TSFSMEDDPQ PVLLDSISVK PNTILLLDTF FF ILIYHGE QIAQWRKAGY QDDPQYADFK ALLEEPKLEA AELLVDRFPL PRFIDTEAGG SQARFLLSKL NPSDNYQDMA RGGSTIVLTD DVSLQNFMTH LQQVAVSGQA MSHHKKRVY PQAQLQYGQN ATPLQQPAQF MPPQDPAAAG MSYGQMGMPP QGAVPSMGQQ QFLTPAQEQL HQQIDQATTS MNDMHLHNVP LVDPNAYMQP QVPVQMGTPL QQQQQPMAAP AYGQPSAAMG QNMRPMNQLY PIDLLTELPP PITDLTLPPP PLVIPPERML VPSELSNASP DYIRSTLNAV PKNSSLLKKS KLPFGLVIRP YQHLYDDIDP P PLNEDGLI VRCRRCRSYM NPFVTFIEQG RRWRCNFCRL ANDVPMQMDQ SDPNDPKSRY DRNEIKCAVM EYMAPKEYTL RQPPPATYCF LIDVSQSSIK SGLLATTINT LLQNLDSIPN HDERTRISIL CVDNAIHYFK IPLDSENNEE SADQINMMDI ADLEEPFLPR PNSMVVSLKA CRQNIETLLT KIPQIFQSNL ITNFALGPAL KSAYHLIGGV GG KIIVVSG TLPNLGIGKL QRRNESGVVN TSKETAQLLS CQDSFYKNFT IDCSKVQITV DLFLASEDYM DVASLSNLSR FTAGQTHFYP GFSGKNPNDI VKFSTEFAKH ISMDFCMETV MRARGSTGLR MSRFYGHFFN RSSDLCAFST MPRDQSYLFE VNVDESIMAD YCYVQVAVLL SLNNSQRRIR IITLAMPTTE SLAEVYASAD QLAIASFYNS KAV EKALNS SLDDARVLIN KSVQDILATY KKEIVVSNTA GGAPLRLCAN LRMFPLLMHS LTKHMAFRSG IVPSDHRASA LNNLESLPLK YLIKNIYPDV YSLHDMADEA GLPVQTEDGE ATGTIVLPQP INATSSLFER YGLYLIDNGN ELFLWMGGDA VPALVFDVFG TQDIFDIPIG KQEIPVVENS EFNQRVRNII NQLRNHDDVI TYQSLYIVRG ASLS EPVNH ASAREVATLR LWASSTLVED KILNNESYRE FLQIMKARIS K MAGWDIFG WFRDVLASLG LWNKHGKLLF LGLDNAGKTT LLHMLKNDRL ATLQPTWHPT SEELAIGNIK FTTFDLGGHI QARRLWKDYF PEVNGIVFLV DAADPERFDE ARVELDALFN IAELKDVPFV ILGNKIDAPN AVSEAELRSA LGLLNTTGSQ RIEGQRPVEV FMCSVVMRNG YLEAFQWLSQ YI

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 3.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 149 / Number images used: 800000
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 100000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2qtv

source_name: PDB, initial_model_type: experimental model

1pcx

source_name: PDB, initial_model_type: experimental model

5kyw

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: OTHER
Output model

PDB-8bsh:
COPII inner coat

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