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- EMDB-21136: Mouse retromer (VPS26/VPS35/VPS29) heterotrimer -

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Basic information

Entry
Database: EMDB / ID: EMD-21136
TitleMouse retromer (VPS26/VPS35/VPS29) heterotrimer
Map dataMouse retromer (VPS26/VPS35/VPS29) heterotrimer
Sample
  • Complex: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
    • Protein or peptide: Vacuolar protein sorting-associated protein 26A
    • Protein or peptide: Vacuolar protein sorting-associated protein 29
Keywordsretromer / membrane trafficking / endosomal trafficking / membrane coat complexes / PROTEIN TRANSPORT
Function / homology
Function and homology information


WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / vacuolar protein processing ...WNT ligand biogenesis and trafficking / neurotransmitter receptor transport, endosome to plasma membrane / negative regulation of protein localization / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / negative regulation of protein homooligomerization / tubular endosome / regulation of terminal button organization / positive regulation of Wnt protein secretion / vacuolar protein processing / retromer, cargo-selective complex / mitochondrion to lysosome vesicle-mediated transport / Golgi to vacuole transport / protein localization to organelle / negative regulation of lysosomal protein catabolic process / positive regulation of locomotion involved in locomotory behavior / negative regulation of late endosome to lysosome transport / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / retromer complex / vesicle-mediated transport in synapse / voluntary musculoskeletal movement / mitochondrial fragmentation involved in apoptotic process / transcytosis / dopaminergic synapse / regulation of synapse maturation / endocytic recycling / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / lysosome organization / positive regulation of mitochondrial fission / regulation of postsynapse assembly / D1 dopamine receptor binding / 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 / protein transport / presynapse / vesicle / early endosome / lysosome / postsynapse / neuron projection / endosome membrane / endosome / postsynaptic density / negative regulation of gene expression / neuronal cell body / synapse / positive regulation of gene expression / perinuclear region of cytoplasm / glutamatergic synapse / mitochondrion / metal ion binding / membrane / cytoplasm / cytosol
Similarity search - Function
Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Arrestin-like, C-terminal ...Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Arrestin-like, C-terminal / Metallo-dependent phosphatase-like / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 26A / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsKendall AK / Jackson LP
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
CitationJournal: 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
DepositionDec 17, 2019-
Header (metadata) releaseFeb 19, 2020-
Map releaseFeb 19, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0148
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0148
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vac
  • Surface level: 0.0148
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21136.png

Downloads & links

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Map

FileDownload / File: emd_21136.map.gz / Format: CCP4 / Size: 46.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMouse retromer (VPS26/VPS35/VPS29) heterotrimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 230 pix.
= 252.08 Å		1.1 Å/pix.
x 230 pix.
= 252.08 Å		1.1 Å/pix.
x 230 pix.
= 252.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0148 / Movie #1: 0.0148
Minimum - Maximum-0.024053138 - 0.08951092
Average (Standard dev.)0.00020330076 (±0.0021895543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions230230230
Spacing230230230
CellA=B=C: 252.07999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0961.0961.096
M x/y/z230230230
origin x/y/z0.0000.0000.000
length x/y/z252.080252.080252.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS230230230
D min/max/mean-0.0240.0900.000

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Supplemental data

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Sample components

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Entire : Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers

EntireName: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
Components
  • Complex: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
    • Protein or peptide: Vacuolar protein sorting-associated protein 26A
    • Protein or peptide: Vacuolar protein sorting-associated protein 29

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Supramolecule #1: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers

SupramoleculeName: Mouse retromer (VPS26/VPS35/VPS29) tetramer of heterotrimers
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Vacuolar protein sorting-associated protein 35

MacromoleculeName: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 91.821727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: Vacuolar protein sorting-associated protein 26A

MacromoleculeName: Vacuolar protein sorting-associated protein 26A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 38.167789 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFLGGFFGP ICEIDVALND GETRKMAEMK TEDGKVEKHY LFYDGESVSG KVNLAFKQPG KRLEHQGIRI EFVGQIELFN DKSNTHEFV NLVKELALPG ELTQSRSYDF EFMQVEKPYE SYIGANVRLR YFLKVTIVRR LTDLVKEYDL IVHQLATYPD V NNSIKMEV ...String:
MSFLGGFFGP ICEIDVALND GETRKMAEMK TEDGKVEKHY LFYDGESVSG KVNLAFKQPG KRLEHQGIRI EFVGQIELFN DKSNTHEFV NLVKELALPG ELTQSRSYDF EFMQVEKPYE SYIGANVRLR YFLKVTIVRR LTDLVKEYDL IVHQLATYPD V NNSIKMEV GIEDCLHIEF EYNKSKYHLK DVIVGKIYFL LVRIKIQHME LQLIKKEITG IGPSTTTETE TIAKYEIMDG AP VKGESIP IRLFLAGYDP TPTMRDVNKK FSVRYFLNLV LVDEEDRRYF KQQEIILWRK APEKLRKQRT NFHQRFESPD SQA SAEQPE M

UniProtKB: Vacuolar protein sorting-associated protein 26A

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Macromolecule #3: Vacuolar protein sorting-associated protein 29

MacromoleculeName: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 20.521668 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 71.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 26369
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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