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Yorodumi- EMDB-12221: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12221 | ||||||||||||||||||
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Title | VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex | ||||||||||||||||||
Map data | Sharpened, locally filtered map of VPS26 dimer region of the metazoan retromer:SNX3 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 / negative regulation of early endosome to late endosome transport / late endosome to Golgi 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 / negative regulation of early endosome to late endosome transport / late endosome to Golgi transport / cadmium ion transmembrane transport / nickel cation transport / solute:proton symporter activity / protein to membrane docking / negative regulation of protein transport / neurotransmitter receptor transport, endosome to plasma membrane / Metal ion SLC transporters / membrane invagination / inorganic cation transmembrane transporter activity / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / zinc ion transmembrane transporter activity / manganese ion transport / tubular endosome / positive regulation of Wnt protein secretion / detection of oxygen / mitochondrion to lysosome vesicle-mediated transport / regulation of terminal button organization / cobalt ion transport / cadmium ion transmembrane transporter activity / WNT ligand biogenesis and trafficking / retromer, cargo-selective complex / manganese ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / regulation of postsynapse assembly / intralumenal vesicle formation / iron import into cell / positive regulation of locomotion involved in locomotory behavior / copper ion transmembrane transporter activity / iron ion transmembrane transporter activity / retromer complex binding / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / iron ion transmembrane transport / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / vesicle-mediated transport in synapse / ferrous iron transmembrane transporter activity / retromer complex / phosphatidylinositol-5-phosphate binding / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / copper ion transport / voluntary musculoskeletal movement / negative regulation of viral entry into host cell / dopaminergic synapse / basal part of cell / regulation of protein metabolic process / D1 dopamine receptor binding / regulation of synapse maturation / transcytosis / early phagosome / endocytic recycling / phosphatidylinositol-3-phosphate binding / regulation of Wnt signaling pathway / retrograde transport, endosome to Golgi / regulation of mitochondrion organization / vacuole / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of protein localization to cell periphery / response to iron ion / negative regulation of phagocytosis / dendrite morphogenesis / clathrin-coated vesicle / heme biosynthetic process / positive regulation of mitochondrial fission / lysosome organization / cadmium ion binding / regulation of presynapse assembly / regulation of macroautophagy / erythrocyte development / intracellular protein transport / Iron uptake and transport / response to bacterium / brush border membrane / protein destabilization / trans-Golgi network / negative regulation of protein catabolic process / modulation of chemical synaptic transmission / regulation of protein stability / recycling endosome / : / Wnt signaling pathway / positive regulation of neuron projection development / negative regulation of inflammatory response / multicellular organismal-level iron ion homeostasis Similarity search - Function | ||||||||||||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | ||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.5 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_12221.map.gz | 3.9 MB | EMDB map data format | |
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Header (meta data) | emd-12221-v30.xml emd-12221.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12221_fsc.xml | 6.1 KB | Display | FSC data file |
Images | emd_12221.png | 97.5 KB | ||
Masks | emd_12221_msk_1.map | 18.1 MB | Mask map | |
Others | emd_12221_half_map_1.map.gz emd_12221_half_map_2.map.gz | 17 MB 17 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12221 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12221 | HTTPS FTP |
-Validation report
Summary document | emd_12221_validation.pdf.gz | 351.1 KB | Display | EMDB validaton report |
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Full document | emd_12221_full_validation.pdf.gz | 350.3 KB | Display | |
Data in XML | emd_12221_validation.xml.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12221 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12221 | HTTPS FTP |
-Related structure data
Related structure data | 7bloMC 7blnC 7blpC 7blqC 7blrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10633 (Title: Cryo-electron tomography of the metazoan membrane-assembled retromer:SNX3 coat containing Wls cargo motif Data size: 764.9 Data #1: Raw image frames for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [micrographs - multiframe] Data #2: Corrected, aligned and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series] Data #3: Corrected, aligned, dose-filtered and order-sorted tilt series for the metazoan retromer:SNX3 coat assembled on the Wls cargo-containing membranes [tilt series]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12221.map.gz / Format: CCP4 / Size: 18.1 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 metazoan retromer:SNX3 assembled on the membrane | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.701 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_12221_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half-map1
File | emd_12221_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_12221_half_map_2.map | ||||||||||||
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Annotation | half-map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c...
Entire | Name: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex |
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Components |
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-Supramolecule #1: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 c...
Supramolecule | Name: VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 cargo-containing complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide. |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Vacuolar protein sorting-associated protein 26A
Macromolecule | Name: Vacuolar protein sorting-associated protein 26A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.364617 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: FGPICEIDIV LNDGETRKMA EMKTEDGKVE KHYLFYDGES VSGKVNLAFK QPGKRLEHQG IRIEFVGQIE LFNDKSNTHE FVNLVKELA LPGELTQSRS YDFEFMQVEK PYESYIGANV RLRYFLKVTI VRRLTDLVKE YDLIVHQLAT YPDVNNSIKM E VGIEDCLH ...String: FGPICEIDIV LNDGETRKMA EMKTEDGKVE KHYLFYDGES VSGKVNLAFK QPGKRLEHQG IRIEFVGQIE LFNDKSNTHE FVNLVKELA LPGELTQSRS YDFEFMQVEK PYESYIGANV RLRYFLKVTI VRRLTDLVKE YDLIVHQLAT YPDVNNSIKM E VGIEDCLH IEFEYNKSKY HLKDVIVGKI YFLLVRIKIQ HMELQLIKKE ITGIGPSTTT ETETIAKYEI MDGAPVKGES IP IRLFLAG YDPTPTMRDV NKKFSVRYFL NLVLVDEEDR RYFKQQEIIL WRKAPEK |
-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: Mus musculus (house mouse) |
Molecular weight | Theoretical: 17.979393 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: TVADTRRLIT KPQNLNDAYG PPSNFLEIDV SNPQTVGVGR GRFTTYEIRV KTNLPIFKLK ESTVRRRYSD FEWLRSELER ESKVVVPPL PGKAFLRQLP FRGDDGIFDD NFIEERKQGL EQFINKVAGH PLAQNERCLH MFLQDEIIDK SYTPSK |
-Macromolecule #3: C-term (residues 493-54) of Wls (fitted sequence corresponds to h...
Macromolecule | Name: C-term (residues 493-54) of Wls (fitted sequence corresponds to hDMT1-II) type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 1.221422 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QPELYLLNTM |
-Macromolecule #4: Vacuolar protein sorting-associated protein 35
Macromolecule | Name: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 40.714016 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QEKLLDEAIQ AVKVQSFQMK RCLDKNKLMD ALKHASNMLG ELRTSMLSPK SYYELYMAIS DELHYLEVYL TDEFAKGRKV ADLYELVQY AGNIIPRLYL LITVGVVYVK SFPQSRKDIL KDLVEMCRGV QHPLRGLFLR NYLLQCTRNI LPDEGEPTDE E TTGDISDS ...String: QEKLLDEAIQ AVKVQSFQMK RCLDKNKLMD ALKHASNMLG ELRTSMLSPK SYYELYMAIS DELHYLEVYL TDEFAKGRKV ADLYELVQY AGNIIPRLYL LITVGVVYVK SFPQSRKDIL KDLVEMCRGV QHPLRGLFLR NYLLQCTRNI LPDEGEPTDE E TTGDISDS MDFVLLNFAE MNKLWVRMQH QGHSRDREKR ERERQELRIL VGTNLVRLSQ LEGVNVERYK QIVLTGILEQ VV NCRDALA QEYLMECIIQ VFPDEFHLQT LNPFLRACAE LHQNVNVKNI IIALIDRLAL FAHREDGPGI PADIKLFDIF SQQ VATVIQ SRQDMPSEDV VSLQVSLINL AMKCYP |
-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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |