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- EMDB-12220: VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12220
TitleVPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex
Map dataLAFTER-filtered map of VP35 arch of metazoan retromer:SNX3 complex
Sample
  • Complex: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.
    • Protein or peptide: Vacuolar protein sorting-associated protein 29
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
Keywordsendosomes / coat proteins / membrane trafficking / cargo-sorting / ENDOCYTOSIS
Function / homology
Function and homology information


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 / 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 / regulation of dendritic spine maintenance / mitochondrion-derived vesicle / 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 / retromer, cargo-selective complex / regulation of postsynapse assembly / positive regulation of locomotion involved in locomotory behavior / negative regulation of lysosomal protein catabolic process / negative regulation of late endosome to lysosome transport / positive regulation of dopamine biosynthetic process / positive regulation of dopamine receptor signaling pathway / vesicle-mediated transport in synapse / retromer complex / mitochondrial fragmentation involved in apoptotic process / protein localization to endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / voluntary musculoskeletal movement / dopaminergic synapse / regulation of protein metabolic process / regulation of synapse maturation / transcytosis / endocytic recycling / regulation of mitochondrion organization / retrograde transport, endosome to Golgi / positive regulation of protein localization to cell periphery / positive regulation of mitochondrial fission / lysosome organization / regulation of presynapse assembly / D1 dopamine receptor binding / regulation of macroautophagy / intracellular protein transport / protein destabilization / modulation of chemical synaptic transmission / regulation of protein stability / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of protein catabolic process / positive regulation of canonical Wnt signaling pathway / late endosome / presynapse / lysosome / postsynaptic density / early endosome / endosome membrane / endosome / neuron projection / lysosomal membrane / negative regulation of gene expression / intracellular membrane-bounded organelle / neuronal cell body / glutamatergic synapse / positive regulation of gene expression / perinuclear region of cytoplasm / extracellular exosome / metal ion binding / cytosol
Similarity search - Function
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 / Metallo-dependent phosphatase-like / Armadillo-type fold
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 8.9 Å
AuthorsLeneva N / Kovtun O
Funding support United Kingdom, 5 items
OrganizationGrant numberCountry
Wellcome Trust207455/Z/17/Z United Kingdom
Wellcome Trust206171/Z/17/Z United Kingdom
Wellcome Trust202905/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/16 United Kingdom
European Research Council (ERC)ERC-CoG-648432 MEMBRANEFUSION United Kingdom
CitationJournal: 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
DepositionJan 18, 2021-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bln
  • Surface level: 0.021
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12220.png

Downloads & links

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Map

FileDownload / File: emd_12220.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLAFTER-filtered map of VP35 arch of metazoan retromer:SNX3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 168 pix.
= 285.768 Å		1.7 Å/pix.
x 168 pix.
= 285.768 Å		1.7 Å/pix.
x 168 pix.
= 285.768 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.701 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021 / Movie #1: 0.021
Minimum - Maximum-0.04694227 - 0.06815528
Average (Standard dev.)0.000087828455 (±0.0027450174)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 285.768 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.7011.7011.701
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z285.768285.768285.768
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS168168168
D min/max/mean-0.0470.0680.000

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Supplemental data

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Mask #1

Fileemd_12220_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map1 of VP35 arch of metazoan retromer:SNX3 complex

Fileemd_12220_half_map_1.map
Annotationhalf-map1 of VP35 arch of metazoan retromer:SNX3 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map2 of VP35 arch of metazoan retromer:SNX3 complex

Fileemd_12220_half_map_2.map
Annotationhalf-map2 of VP35 arch of metazoan retromer:SNX3 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.

EntireName: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.
Components
  • Complex: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.
    • Protein or peptide: Vacuolar protein sorting-associated protein 29
    • Protein or peptide: Vacuolar protein sorting-associated protein 35

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Supramolecule #1: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.

SupramoleculeName: arch assembly (VPS35/VPS29) of the metazoan retromer:SNX3 complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: metazoan retromer:SNX3 complex assembled on liposomes containing Wls cargo peptide.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Vacuolar protein sorting-associated protein 29

MacromoleculeName: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.531705 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 YKKP

UniProtKB: Vacuolar protein sorting-associated protein 29

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Macromolecule #2: Vacuolar protein sorting-associated protein 35

MacromoleculeName: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.816805 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 DIKLFD IFSQQVATVI QSRQDMPSED VVSLQVSLIN LAMKCYPDRV DYVDKVLETT VEIFNKLNLE HIATSSAVSK ELTR LLKIP VDTYNNILTV LKLKHFHPLF EYFDYESRKS MSCYVLSNVL DYNTEIVSQD QVDSIMNLVS TLIQDQPDQP VEDPD PEDF ADEQSLVGRF IHLLRSEDPD QQYLILNTAR KHFGAGGNQR IRFTLPPLVF AAYQLAFRYK ENSKVDDKWE 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 NTLEHLRLRR ESPESEGPIY EGLIL

UniProtKB: Vacuolar protein sorting-associated protein 35

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 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

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 89313
ExtractionNumber tomograms: 113 / Number images used: 822112
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

2r17

chain_id: A, source_name: PDB, initial_model_type: experimental model

5f0l

chain_id: A, source_name: PDB, initial_model_type: experimental model

2r17

chain_id: B, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7bln:
VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins

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