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Yorodumi- EMDB-12224: Vps26 dimer region of the fungal membrane-assembled retromer:Grd1... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12224 | ||||||||||||||||||
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Title | Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 complex. | ||||||||||||||||||
Map data | Sharpened, locally filtered map of VPS26 dimer region of the fungal retromer:Grd19 complex assembled on the membrane | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / nickel cation transmembrane transporter activity / lead ion transport / cadmium ion transmembrane transport / nickel cation transport ...vanadium ion transmembrane transporter activity / vanadium ion transport / transition metal ion transmembrane transporter activity / paraferritin complex / Defective SLC11A2 causes hypochromic microcytic anemia, with iron overload 1 (AHMIO1) / lead ion transmembrane transporter activity / nickel cation transmembrane transporter activity / lead ion transport / cadmium ion transmembrane transport / nickel cation transport / solute:proton symporter activity / inorganic cation transmembrane transporter activity / Metal ion SLC transporters / manganese ion transport / iron ion transmembrane transport / manganese ion transmembrane transporter activity / zinc ion transmembrane transporter activity / detection of oxygen / iron ion transmembrane transporter activity / cadmium ion transmembrane transporter activity / cobalt ion transport / retromer, cargo-selective complex / cobalt ion transmembrane transporter activity / iron import into cell / retromer complex binding / copper ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / copper ion transport / basal part of cell / phosphatidylinositol-3-phosphate binding / vacuole / retrograde transport, endosome to Golgi / response to iron ion / dendrite morphogenesis / heme biosynthetic process / erythrocyte development / cadmium ion binding / brush border membrane / Iron uptake and transport / intracellular protein transport / trans-Golgi network / recycling endosome / multicellular organismal-level iron ion homeostasis / recycling endosome membrane / activation of cysteine-type endopeptidase activity involved in apoptotic process / extracellular vesicle / protein transport / late endosome / apical part of cell / late endosome membrane / cellular response to oxidative stress / iron ion transport / cytoplasmic vesicle / early endosome membrane / intracellular iron ion homeostasis / mitochondrial outer membrane / lysosome / response to hypoxia / learning or memory / early endosome / apical plasma membrane / lysosomal membrane / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / mitochondrion / membrane / nucleus / plasma membrane / cytosol / cytoplasm 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: 9.2 Å | ||||||||||||||||||
Authors | Leneva N / Kovtun O / Morado DR / Briggs JAG / Owen DJ | ||||||||||||||||||
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_12224.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-12224-v30.xml emd-12224.xml | 19 KB 19 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12224_fsc.xml | 3.7 KB | Display | FSC data file |
Images | emd_12224.png | 98.3 KB | ||
Masks | emd_12224_msk_1.map | 3.8 MB | Mask map | |
Others | emd_12224_half_map_1.map.gz emd_12224_half_map_2.map.gz | 3 MB 3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12224 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12224 | HTTPS FTP |
-Related structure data
Related structure data | 7blqMC 7blnC 7bloC 7blpC 7blrC M: atomic model generated by this map C: citing same article (ref.) |
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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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-Map
File | Download / File: emd_12224.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened, locally filtered map of VPS26 dimer region of the fungal retromer:Grd19 complex assembled on the membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_12224_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map2
File | emd_12224_half_map_1.map | ||||||||||||
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Annotation | half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half-map1
File | emd_12224_half_map_2.map | ||||||||||||
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Annotation | half-map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Vps26 dimer region of the fungal membrane-assembled retromer:Grd1...
Entire | Name: Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 cargo-containing complex |
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Components |
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-Supramolecule #1: Vps26 dimer region of the fungal membrane-assembled retromer:Grd1...
Supramolecule | Name: Vps26 dimer region of the fungal membrane-assembled retromer:Grd19 cargo-containing complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 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) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-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: 34.014195 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: RLLEDALIAV RQQTAMMRKF LDTPGKLMDA LKCCSTLVSE LRTSSLSPKQ YYELYMAVFD ALRYLSAHLR ENHPVNHLAD LYELVQYAG NIIPRLYLMI TVGTAYMSID GAPVKELMKD MMDMSRGVQH PVRGLFLRYY LSGQARDYLP TGDSDGPEGN L QDSINFIL ...String: RLLEDALIAV RQQTAMMRKF LDTPGKLMDA LKCCSTLVSE LRTSSLSPKQ YYELYMAVFD ALRYLSAHLR ENHPVNHLAD LYELVQYAG NIIPRLYLMI TVGTAYMSID GAPVKELMKD MMDMSRGVQH PVRGLFLRYY LSGQARDYLP TGDSDGPEGN L QDSINFIL TNFVEMNKLW VRLQHQGHSR ERDLRTQERR ELQLLVGSNI VRLSQLVDLP TYRDSILGPL LEQIVQCRDI LA QEYLLEV ITQVFPDEYH LHTLDQFLGA VSRLNPHVNV KAIVIGMMNR LSDYAERE |
-Macromolecule #2: Sorting nexin-3
Macromolecule | Name: Sorting nexin-3 / 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: 13.52549 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: PPENFLEIEV RNPQTHGVGR HMYTDYEIVC RTNIPAFKLR QSSVRRRYSD FEYFRDILER ESARVTIPPL PGKVFTNRFS DEVIENRRA GLEKFLKIVV GHPLLQTGSK VLAAFVQ |
-Macromolecule #3: Vacuolar protein sorting-associated protein 26-like protein
Macromolecule | Name: Vacuolar protein sorting-associated protein 26-like protein type: protein_or_peptide / ID: 3 / 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: 34.308449 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: FSTPVDIDIV LADADKRAMV DVKLDKNRRE KVPLYMDGES VKGCVTVRPK DGKRLEHTGI KVQFIGTIEM FFDRGNHYEF LSLVQELAA PGELQHPQTF DFNFKNVEKQ YESYNGINVK LRYFVRVTVS RRMADVIREK DIWVYSYRIP PELNSSIKMD V GIEDCLHI ...String: FSTPVDIDIV LADADKRAMV DVKLDKNRRE KVPLYMDGES VKGCVTVRPK DGKRLEHTGI KVQFIGTIEM FFDRGNHYEF LSLVQELAA PGELQHPQTF DFNFKNVEKQ YESYNGINVK LRYFVRVTVS RRMADVIREK DIWVYSYRIP PELNSSIKMD V GIEDCLHI EFEYSKSKYH LKDVIVGRIY FLLVRLKIKH MELSIIRRET TGVAPNQYNE SETLVRFEIM DGSPSRGETI PI RLFLGGF DLTPTFRDVN KKFSTRYYLS LVLIDEDARR YFKQSEIILY RQPPE |
-Macromolecule #4: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sor...
Macromolecule | Name: The C-terminal portion of Kex2 cargo, fitted with Phi-X-(L/M) sorting motif of hDMT1-II cargo. type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus) |
Molecular weight | Theoretical: 1.221422 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QPELYLLNTM |
-Macromolecule #5: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOX...
Macromolecule | Name: 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE type: ligand / ID: 5 / Number of copies: 2 / Formula: PIB |
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Molecular weight | Theoretical: 554.374 Da |
-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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |