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Yorodumi- EMDB-24963: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the presence o... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24963 | |||||||||
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Title | Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the presence of cyclic peptide RTL4 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / mitochondrion-derived vesicle / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / regulation of terminal button organization ...WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / mitochondrion-derived vesicle / regulation of dendritic spine maintenance / negative regulation of protein homooligomerization / tubular endosome / positive regulation of Wnt protein secretion / mitochondrion to lysosome vesicle-mediated transport / regulation of terminal button organization / regulation of postsynapse assembly / vacuolar protein processing / retromer, cargo-selective complex / protein localization to organelle / positive regulation of locomotion involved in locomotory behavior / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / vesicle-mediated transport in synapse / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / Golgi to vacuole transport / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / voluntary musculoskeletal movement / dopaminergic synapse / D1 dopamine receptor binding / 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 / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / vesicle / postsynapse / early endosome / postsynaptic density / lysosome / endosome membrane / endosome / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.9 Å | |||||||||
Authors | Kendall AK / Jackson LP | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Sci Adv / Year: 2021 Title: De novo macrocyclic peptides for inhibiting, stabilizing, and probing the function of the retromer endosomal trafficking complex. Authors: Kai-En Chen / Qian Guo / Timothy A Hill / Yi Cui / Amy K Kendall / Zhe Yang / Ryan J Hall / Michael D Healy / Joanna Sacharz / Suzanne J Norwood / Sachini Fonseka / Boyang Xie / Robert C ...Authors: Kai-En Chen / Qian Guo / Timothy A Hill / Yi Cui / Amy K Kendall / Zhe Yang / Ryan J Hall / Michael D Healy / Joanna Sacharz / Suzanne J Norwood / Sachini Fonseka / Boyang Xie / Robert C Reid / Natalya Leneva / Robert G Parton / Rajesh Ghai / David A Stroud / David P Fairlie / Hiroaki Suga / Lauren P Jackson / Rohan D Teasdale / Toby Passioura / Brett M Collins / Abstract: The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and ...The retromer complex (Vps35-Vps26-Vps29) is essential for endosomal membrane trafficking and signaling. Mutation of the retromer subunit Vps35 causes late-onset Parkinson’s disease, while viral and bacterial pathogens can hijack the complex during cellular infection. To modulate and probe its function, we have created a novel series of macrocyclic peptides that bind retromer with high affinity and specificity. Crystal structures show that most of the cyclic peptides bind to Vps29 via a Pro-Leu–containing sequence, structurally mimicking known interactors such as TBC1D5 and blocking their interaction with retromer in vitro and in cells. By contrast, macrocyclic peptide RT-L4 binds retromer at the Vps35-Vps26 interface and is a more effective molecular chaperone than reported small molecules, suggesting a new therapeutic avenue for targeting retromer. Last, tagged peptides can be used to probe the cellular localization of retromer and its functional interactions in cells, providing novel tools for studying retromer function. | |||||||||
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_24963.map.gz | 149.9 MB | EMDB map data format | |
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Header (meta data) | emd-24963-v30.xml emd-24963.xml | 13.4 KB 13.4 KB | Display Display | EMDB header |
Images | emd_24963.png | 89.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24963 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24963 | HTTPS FTP |
-Validation report
Summary document | emd_24963_validation.pdf.gz | 303.7 KB | Display | EMDB validaton report |
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Full document | emd_24963_full_validation.pdf.gz | 303.3 KB | Display | |
Data in XML | emd_24963_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_24963_validation.cif.gz | 7.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24963 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24963 | HTTPS FTP |
-Related 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_24963.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6811 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) heterotrimer in the presence o...
Entire | Name: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the presence of cyclic peptide RTL4 |
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Components |
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-Supramolecule #1: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the presence o...
Supramolecule | Name: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer in the presence of cyclic peptide RTL4 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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 35
Macromolecule | Name: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPTTQQSPQD EQEKLLDEAI QAVKVQSFQM KRCLDKNKLM DALKHASNML GELRTSMLSP KSYYELYMA ISDELHYLEV YLTDEFAKGR KVADLYELVQ YAGNIIPRLY LLITVGVVYV K SFPQSRKD ILKDLVEMCR GVQHPLRGLF LRNYLLQCTR NILPDEGEPT ...String: MPTTQQSPQD EQEKLLDEAI QAVKVQSFQM KRCLDKNKLM DALKHASNML GELRTSMLSP KSYYELYMA ISDELHYLEV YLTDEFAKGR KVADLYELVQ YAGNIIPRLY LLITVGVVYV K SFPQSRKD ILKDLVEMCR GVQHPLRGLF LRNYLLQCTR NILPDEGEPT DEETTGDISD SM DFVLLNF AEMNKLWVRM QHQGHSRDRE KRERERQELR ILVGTNLVRL SQLEGVNVER YKQ IVLTGI LEQVVNCRDA LAQEYLMECI IQVFPDEFHL QTLNPFLRAC AELHQNVNVK NIII ALIDR LALFAHREDG PGIPAEIKLF DIFSQQVATV IQSRQDMPSE DVVSLQVSLI NLAMK CYPD RVDYVDKVLE TTVEIFNKLN LEHIATSSAV SKELTRLLKI PVDTYNNILT VLKLKH FHP LFEYFDYESR KSMSCYVLSN VLDYNTEIVS QDQVDSIMNL VSTLIQDQPD QPVEDPD PE DFADEQSLVG RFIHLLRSDD PDQQYLILNT ARKHFGAGGN QRIRFTLPPL VFAAYQLA F RYKENSQMDD KWEKKCQKIF SFAHQTISAL IKAELAELPL RLFLQGALAA GEIGFENHE TVAYEFMSQA FSLYEDEISD SKAQLAAITL IIGTFERMKC FSEENHEPLR TQCALAASEL LEEPDQGRA VSTCAHLFWS GRNTDKNGEE LHGGKRVMEC LKKALKIANQ CMDPSLQVQL F IEILNRYI YFYEKENDAV TIQVLNQLIQ KIREDLPNLE SSEETEQINK HFHNTLEHLR SR RESPESE GPIYEGLIL |
-Macromolecule #2: Vacuolar protein sorting-associated protein 26A
Macromolecule | Name: Vacuolar protein sorting-associated protein 26A / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSFLGGFFGP ICEIDVALND GETRKMAEMK TEDGKVEKHY LFYDGESVSG KVNLAFKQPG KRLEHQGIR IEFVGQIELF NDKSNTHEFV NLVKELALPG ELTQSRSYDF EFMQVEKPYE S YIGANVRL RYFLKVTIVR RLTDLVKEYD LIVHQLATYP DVNNSIKMEV ...String: MSFLGGFFGP ICEIDVALND GETRKMAEMK TEDGKVEKHY LFYDGESVSG KVNLAFKQPG KRLEHQGIR IEFVGQIELF NDKSNTHEFV NLVKELALPG ELTQSRSYDF EFMQVEKPYE S YIGANVRL RYFLKVTIVR RLTDLVKEYD LIVHQLATYP DVNNSIKMEV GIEDCLHIEF EY NKSKYHL KDVIVGKIYF LLVRIKIQHM ELQLIKKEIT GIGPSTTTET ETIAKYEIMD GAP VKGESI PIRLFLAGYD PTPTMRDVNK KFSVRYFLNL VLVDEEDRRY FKQQEIILWR KAPE KLRKQ RTNFHQRFES PDSQASAEQP EM |
-Macromolecule #3: Vacuolar protein sorting-associated protein 29
Macromolecule | Name: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLVLVLGDLH IPHRCNSLPA KFKKLLVPGK IQHILCTGNL CTKESYDYLK TLAGDVHIVR GDFDENLNY PEQKVVTVGQ FKIGLIHGHQ VIPWGDMASL ALLQRQFDVD ILISGHTHKF E AFEHENKF YINPGSATGA YNALET |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 28083 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |