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Yorodumi- EMDB-12223: Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12223 | ||||||||||||||||||
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Title | Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex | ||||||||||||||||||
Map data | LAFTER-filtered map of Vps35/Vps29 arch of fungal retromer:Grd19 complex on the membrane | ||||||||||||||||||
Sample |
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Keywords | endosomes / coat proteins / membrane trafficking / cargo-sorting / ENDOCYTOSIS | ||||||||||||||||||
Function / homology | Function and homology information retromer, cargo-selective complex / retromer complex / retrograde transport, endosome to Golgi / protein transport / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.5 Å | ||||||||||||||||||
Authors | Leneva N / Kovtun O | ||||||||||||||||||
Funding support | United Kingdom, 5 items
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Citation | Journal: Sci Adv / Year: 2021 Title: Architecture and mechanism of metazoan retromer:SNX3 tubular coat assembly. Authors: Natalya Leneva / Oleksiy Kovtun / Dustin R Morado / John A G Briggs / David J Owen / Abstract: Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core ...Retromer is a master regulator of cargo retrieval from endosomes, which is critical for many cellular processes including signaling, immunity, neuroprotection, and virus infection. The retromer core (VPS26/VPS29/VPS35) is present on cargo-transporting, tubular carriers along with a range of sorting nexins. Here, we elucidate the structural basis of membrane tubulation and coupled cargo recognition by metazoan and fungal retromer coats assembled with the non-Bin1/Amphiphysin/Rvs (BAR) sorting nexin SNX3 using cryo-electron tomography. The retromer core retains its arched, scaffolding structure but changes its mode of membrane recruitment when assembled with different SNX adaptors, allowing cargo recognition at subunit interfaces. Thus, membrane bending and cargo incorporation can be modulated to allow retromer to traffic cargoes along different cellular transport routes. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12223.map.gz | 4.1 MB | EMDB map data format | |
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Header (meta data) | emd-12223-v30.xml emd-12223.xml | 17.3 KB 17.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12223_fsc.xml | 3.8 KB | Display | FSC data file |
Images | emd_12223.png | 102.6 KB | ||
Masks | emd_12223_msk_1.map | 4.3 MB | Mask map | |
Filedesc metadata | emd-12223.cif.gz | 6 KB | ||
Others | emd_12223_half_map_1.map.gz emd_12223_half_map_2.map.gz | 4.1 MB 4.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12223 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12223 | HTTPS FTP |
-Validation report
Summary document | emd_12223_validation.pdf.gz | 587.1 KB | Display | EMDB validaton report |
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Full document | emd_12223_full_validation.pdf.gz | 586.6 KB | Display | |
Data in XML | emd_12223_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | emd_12223_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12223 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12223 | HTTPS FTP |
-Related structure data
Related structure data | 7blpMC 7blnC 7bloC 7blqC 7blrC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10631 (Title: Cryo-electron tomography of the fungal membrane-assembled retromer:Grd19 coat containing Kex2 cargo motif Data size: 347.7 Data #1: Raw image frames for the fungal retromer:Grd19 coat assembled on the Kex2 cargo-containing membranes [micrographs - multiframe] Data #2: Corrected, aligned and order-sorted tilt series for the membrane-reconstituted fungal retromer:Grd19 complex in the presence of cargo-signal containing C-portion of the Kex2 cargo. [tilt series] Data #3: Corrected, aligned, dose-filtered and order-sorted tilt series for the membrane-reconstituted fungal retromer:Grd19 complex in the presence of cargo-signal containing C-portion of the Kex2 cargo. [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12223.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | LAFTER-filtered map of Vps35/Vps29 arch of fungal retromer:Grd19 complex on the membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.758 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12223_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map1
File | emd_12223_half_map_1.map | ||||||||||||
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Annotation | half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map2
File | emd_12223_half_map_2.map | ||||||||||||
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Annotation | half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex.
Entire | Name: Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex. |
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Components |
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-Supramolecule #1: Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex.
Supramolecule | Name: Vps35/Vps29 arch of fungal membrane-assembled retromer:Grd19 complex. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: fungal retromer:Grd19 complex assembled on liposomes containing Kex2 cargo peptide. |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
-Macromolecule #1: Vacuolar protein sorting-associated protein 35
Macromolecule | Name: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 98.566781 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSTPAPPEEQ ARLLEDALIA VRQQTAMMRK FLDTPGKLMD ALKCCSTLVS ELRTSSLSPK QYYELYMAVF DALRYLSAHL RENHPVNHL ADLYELVQYA GNIIPRLYLM ITVGTAYMSI DGAPVKELMK DMMDMSRGVQ HPVRGLFLRY YLSGQARDYL P TGDSDGPE ...String: MSTPAPPEEQ ARLLEDALIA VRQQTAMMRK FLDTPGKLMD ALKCCSTLVS ELRTSSLSPK QYYELYMAVF DALRYLSAHL RENHPVNHL ADLYELVQYA GNIIPRLYLM ITVGTAYMSI DGAPVKELMK DMMDMSRGVQ HPVRGLFLRY YLSGQARDYL P TGDSDGPE GNLQDSINFI LTNFVEMNKL WVRLQHQGHS RERDLRTQER RELQLLVGSN IVRLSQLVDL PTYRDSILGP LL EQIVQCR DILAQEYLLE VITQVFPDEY HLHTLDQFLG AVSRLNPHVN VKAIVIGMMN RLSDYAERES QNEPEEDRAK LEE EALAKL LEKTKLGQNS ELEPQNGDHP DTEVSSTTDS AQAPSTADSD TTAVNGEEEP VRKRRGIPVN VPLYDIFFDQ VQHL VQAQH LPIQDTIALC CSLANLSLNI YPERLDYVDG ILAYALAKVK EHANSADLHS QPAQQSLLSL LQSPLRRYVS IFTAL SLPT YVSLFQAQTY PTRRAIAGEI VRTLLKNQTL ISTPAHLENV LEILKVLIKE GSQPPAGYPG VVQPRARPLE TDETME EQG WLARLVHLIH SDDNDTQFRL LQMTRKAYAE GNERIRTTTP PLITAGLKLA RRFKAREHYD DNWSSQSSSL FKFLHSA IS TLYTRVNGPG VADLCLRLFC SCGQVADMTE FEEVAYEFFA QAFTVYEESI SDSKAQFQAV CVIASALHRT RNFGRENY D TLITKCAQHA SKLLRKPDQC RAVYLASHLW WATPIAARGE TEDTELYRDG KRVLECLQRA LRVADSCMET ATSIELFVE ILDRYVYYFD QRNESVTTKY LNGLIELIHS NLAGNQQDSA SVEASRKHFI QTLEMIQSKE FEGIVVAPK UniProtKB: Vacuolar protein sorting-associated protein 35 |
-Macromolecule #2: Vacuolar protein sorting-associated protein 29
Macromolecule | Name: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus) Strain: DSM 1495 / CBS 144.50 / IMI 039719 |
Molecular weight | Theoretical: 22.330602 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SMAFLILVIG NLHIPDRALD IPPKFKKLLS PGKISQTLCL GNLTDRATYD YLRSISPDLK IVRGRMDVEA TSLPLMQVVT HGSLRIGFL EGFTLVSEEP DVLLAEANKL DVDVLCWAGG SHRFECFEYM DKFFVNPGSA TGAFTTDWLA EGEEVVPSFC L MDVQGISL ...String: SMAFLILVIG NLHIPDRALD IPPKFKKLLS PGKISQTLCL GNLTDRATYD YLRSISPDLK IVRGRMDVEA TSLPLMQVVT HGSLRIGFL EGFTLVSEEP DVLLAEANKL DVDVLCWAGG SHRFECFEYM DKFFVNPGSA TGAFTTDWLA EGEEVVPSFC L MDVQGISL TLYVYQLRKD ENGTENVAVE KVTYTKPVEP TGAS UniProtKB: Vacuolar protein sorting-associated protein 29 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 3D array |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |