+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21135 | |||||||||
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Title | Mouse retromer sub-structure: VPS35/VPS35 flat dimer | |||||||||
Map data | Mouse retromer sub-structure: VPS35/VPS35 flat dimer | |||||||||
Sample |
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Keywords | retromer / membrane trafficking / endosomal trafficking / membrane coat complexes / PROTEIN TRANSPORT | |||||||||
Function / homology | Function and homology information WNT ligand biogenesis and trafficking / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion ...WNT ligand biogenesis and trafficking / positive regulation of locomotion involved in locomotory behavior / neurotransmitter receptor transport, endosome to plasma membrane / mitochondrion-derived vesicle / negative regulation of protein localization / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / mitochondrion to lysosome vesicle-mediated transport / positive regulation of Wnt protein secretion / regulation of postsynapse assembly / regulation of terminal button organization / retromer, cargo-selective complex / vacuolar protein processing / vesicle-mediated transport in synapse / protein localization to organelle / negative regulation of late endosome to lysosome transport / negative regulation of lysosomal protein catabolic process / positive regulation of dopamine receptor signaling pathway / positive regulation of dopamine biosynthetic process / Golgi to vacuole transport / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / dopaminergic synapse / voluntary musculoskeletal movement / regulation of synapse maturation / transcytosis / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / positive regulation of mitochondrial fission / lysosome organization / D1 dopamine receptor binding / intracellular protein transport / negative regulation of inflammatory response / protein destabilization / modulation of chemical synaptic transmission / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / late endosome / presynapse / postsynapse / endosome / endosome membrane / postsynaptic density / early endosome / lysosome / neuron projection / negative regulation of gene expression / neuronal cell body / glutamatergic synapse / synapse / positive regulation of gene expression / perinuclear region of cytoplasm / mitochondrion / membrane / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | |||||||||
Authors | Kendall AK / Jackson LP | |||||||||
Funding support | 1 items
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Citation | Journal: Structure / Year: 2020 Title: Mammalian Retromer Is an Adaptable Scaffold for Cargo Sorting from Endosomes. Authors: Amy K Kendall / Boyang Xie / Peng Xu / Jue Wang / Rodger Burcham / Meredith N Frazier / Elad Binshtein / Hui Wei / Todd R Graham / Terunaga Nakagawa / Lauren P Jackson / Abstract: Metazoan retromer (VPS26/VPS35/VPS29) associates with sorting nexins on endosomal tubules to sort proteins to the trans-Golgi network or plasma membrane. Mechanisms of metazoan retromer assembly ...Metazoan retromer (VPS26/VPS35/VPS29) associates with sorting nexins on endosomal tubules to sort proteins to the trans-Golgi network or plasma membrane. Mechanisms of metazoan retromer assembly remain undefined. We combine single-particle cryoelectron microscopy with biophysical methods to uncover multiple oligomer structures. 2D class averages reveal mammalian heterotrimers; dimers of trimers; tetramers of trimers; and flat chains. These species are further supported by biophysical solution studies. We provide reconstructions of all species, including key sub-structures (∼5 Å resolution). Local resolution variation suggests that heterotrimers and dimers adopt multiple conformations. Our structures identify a flexible, highly conserved electrostatic dimeric interface formed by VPS35 subunits. We generate structure-based mutants to disrupt this interface in vitro. Equivalent mutations in yeast demonstrate a mild cargo-sorting defect. Our data suggest the metazoan retromer is an adaptable and plastic scaffold that accommodates interactions with different sorting nexins to sort multiple cargoes from endosomes their final destinations. | |||||||||
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_21135.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-21135-v30.xml emd-21135.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21135_fsc.xml | 5.9 KB | Display | FSC data file |
Images | emd_21135.png | 164.2 KB | ||
Filedesc metadata | emd-21135.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21135 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21135 | HTTPS FTP |
-Validation report
Summary document | emd_21135_validation.pdf.gz | 386.8 KB | Display | EMDB validaton report |
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Full document | emd_21135_full_validation.pdf.gz | 386.3 KB | Display | |
Data in XML | emd_21135_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | emd_21135_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21135 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21135 | HTTPS FTP |
-Related structure data
Related structure data | 6vabMC 6vacC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_21135.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mouse retromer sub-structure: VPS35/VPS35 flat dimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.096 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
Entire | Name: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers |
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Components |
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-Supramolecule #1: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
Supramolecule | Name: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Vacuolar protein sorting-associated protein 29
Macromolecule | Name: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 20.521668 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNYP EQKVVTVGQF KIGLIHGHQ VIPWGDMASL ALLQRQFDVD ILISGHTHKF EAFEHENKFY INPGSATGAY NALETNIIPS FVLMDIQAST V VTYVYQLI GDDVKVERIE YKKS UniProtKB: Vacuolar protein sorting-associated protein 29 |
-Macromolecule #2: Vacuolar protein sorting-associated protein 35
Macromolecule | Name: Vacuolar protein sorting-associated protein 35 / 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: 91.821727 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPTTQQSPQD EQEKLLDEAI QAVKVQSFQM KRCLDKNKLM DALKHASNML GELRTSMLSP KSYYELYMAI SDELHYLEVY LTDEFAKGR KVADLYELVQ YAGNIIPRLY LLITVGVVYV KSFPQSRKDI LKDLVEMCRG VQHPLRGLFL RNYLLQCTRN I LPDEGEPT ...String: MPTTQQSPQD EQEKLLDEAI QAVKVQSFQM KRCLDKNKLM DALKHASNML GELRTSMLSP KSYYELYMAI SDELHYLEVY LTDEFAKGR KVADLYELVQ YAGNIIPRLY LLITVGVVYV KSFPQSRKDI LKDLVEMCRG VQHPLRGLFL RNYLLQCTRN I LPDEGEPT DEETTGDISD SMDFVLLNFA EMNKLWVRMQ HQGHSRDREK RERERQELRI LVGTNLVRLS QLEGVNVERY KQ IVLTGIL EQVVNCRDAL AQEYLMECII QVFPDEFHLQ TLNPFLRACA ELHQNVNVKN IIIALIDRLA LFAHREDGPG IPA EIKLFD IFSQQVATVI QSRQDMPSED VVSLQVSLIN LAMKCYPDRV DYVDKVLETT VEIFNKLNLE HIATSSAVSK ELTR LLKIP VDTYNNILTV LKLKHFHPLF EYFDYESRKS MSCYVLSNVL DYNTEIVSQD QVDSIMNLVS TLIQDQPDQP VEDPD PEDF ADEQSLVGRF IHLLRSDDPD QQYLILNTAR KHFGAGGNQR IRFTLPPLVF AAYQLAFRYK ENSQMDDKWE KKCQKI FSF AHQTISALIK AELAELPLRL FLQGALAAGE IGFENHETVA YEFMSQAFSL YEDEISDSKA QLAAITLIIG TFERMKC FS EENHEPLRTQ CALAASKLLK KPDQGRAVST CAHLFWSGRN TDKNGEELHG GKRVMECLKK ALKIANQCMD PSLQVQLF I EILNRYIYFY EKENDAVTIQ VLNQLIQKIR EDLPNLESSE ETEQINKHFH NTLEHLRSRR ESPESEGPIY EGLIL UniProtKB: Vacuolar protein sorting-associated protein 35 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 8.2 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.0 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 |