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- EMDB-12226: Vps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-... -

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Basic information

Entry
Database: EMDB / ID: EMD-12226
TitleVps35/Vps29 arch of fungal membrane-assembled retromer:Vps5 (SNX-BAR) complex.
Map dataLAFTER-filtered map of Vps35/Vps29 arch of fungal retromer:Vps5 assembled on the membrane
Sample
  • Complex: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.
    • Protein or peptide: Vacuolar protein sorting-associated protein 35Vacuole
    • Protein or peptide: Vacuolar protein sorting-associated protein 29Vacuole
Keywordsendosomes / coat proteins / membrane trafficking / cargo-sorting / ENDOCYTOSIS
Function / homology
Function and homology information


retromer, cargo-selective complex / retromer complex / retrograde transport, endosome to Golgi / protein transport / 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
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29 / Vacuolar protein sorting-associated protein 35
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 9.3 Å
AuthorsLeneva N / Kovtun O / Morado DR / Briggs JAG / Owen DJ
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: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7blr
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12226.png

Downloads & links

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Map

FileDownload / File: emd_12226.map.gz / Format: CCP4 / Size: 4.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLAFTER-filtered map of Vps35/Vps29 arch of fungal retromer:Vps5 assembled on the membrane
Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.07783086 - 0.09745563
Average (Standard dev.)0.0001849686 (±0.0041534207)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions104104104
Spacing104104104
CellA=B=C: 280.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z104104104
origin x/y/z0.0000.0000.000
length x/y/z280.800280.800280.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS104104104
D min/max/mean-0.0780.0970.000

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Supplemental data

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Mask #1

Fileemd_12226_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map2

Fileemd_12226_half_map_1.map
Annotationhalf-map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map1

Fileemd_12226_half_map_2.map
Annotationhalf-map1
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 fungal retromer:Vps5 complex.

EntireName: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.
Components
  • Complex: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.
    • Protein or peptide: Vacuolar protein sorting-associated protein 35Vacuole
    • Protein or peptide: Vacuolar protein sorting-associated protein 29Vacuole

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Supramolecule #1: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.

SupramoleculeName: arch assembly (Vps35/Vps29) of the fungal retromer:Vps5 complex.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: fungal retromer:Vps5 complex assembled on liposomes.
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 98.566781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSTPAPPEEQ ARLLEDALIA VRQQTAMMRK FLDTPGKLMD ALKCCSTLVS ELRTSSLSPK QYYELYMAVF DALRYLSAHL RENHPVNHL ADLYELVQYA GNIIPRLYLM ITVGTAYMSI DGAPVKELMK DMMDMSRGVQ HPVRGLFLRY YLSGQARDYL P TGDSDGPE ...String:
MSTPAPPEEQ ARLLEDALIA VRQQTAMMRK FLDTPGKLMD ALKCCSTLVS ELRTSSLSPK QYYELYMAVF DALRYLSAHL RENHPVNHL ADLYELVQYA GNIIPRLYLM ITVGTAYMSI DGAPVKELMK DMMDMSRGVQ HPVRGLFLRY YLSGQARDYL P TGDSDGPE GNLQDSINFI LTNFVEMNKL WVRLQHQGHS RERDLRTQER RELQLLVGSN IVRLSQLVDL PTYRDSILGP LL EQIVQCR DILAQEYLLE VITQVFPDEY HLHTLDQFLG AVSRLNPHVN VKAIVIGMMN RLSDYAERES QNEPEEDRAK LEE EALAKL LEKTKLGQNS ELEPQNGDHP DTEVSSTTDS AQAPSTADSD TTAVNGEEEP VRKRRGIPVN VPLYDIFFDQ VQHL VQAQH LPIQDTIALC CSLANLSLNI YPERLDYVDG ILAYALAKVK EHANSADLHS QPAQQSLLSL LQSPLRRYVS IFTAL SLPT YVSLFQAQTY PTRRAIAGEI VRTLLKNQTL ISTPAHLENV LEILKVLIKE GSQPPAGYPG VVQPRARPLE TDETME EQG WLARLVHLIH SDDNDTQFRL LQMTRKAYAE GNERIRTTTP PLITAGLKLA RRFKAREHYD DNWSSQSSSL FKFLHSA IS TLYTRVNGPG VADLCLRLFC SCGQVADMTE FEEVAYEFFA QAFTVYEESI SDSKAQFQAV CVIASALHRT RNFGRENY D TLITKCAQHA SKLLRKPDQC RAVYLASHLW WATPIAARGE TEDTELYRDG KRVLECLQRA LRVADSCMET ATSIELFVE ILDRYVYYFD QRNESVTTKY LNGLIELIHS NLAGNQQDSA SVEASRKHFI QTLEMIQSKE FEGIVVAPK

UniProtKB: Vacuolar protein sorting-associated protein 35

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Macromolecule #2: Vacuolar protein sorting-associated protein 29

MacromoleculeName: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 22.330602 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMAFLILVIG NLHIPDRALD IPPKFKKLLS PGKISQTLCL GNLTDRATYD YLRSISPDLK IVRGRMDVEA TSLPLMQVVT HGSLRIGFL EGFTLVSEEP DVLLAEANKL DVDVLCWAGG SHRFECFEYM DKFFVNPGSA TGAFTTDWLA EGEEVVPSFC L MDVQGISL ...String:
SMAFLILVIG NLHIPDRALD IPPKFKKLLS PGKISQTLCL GNLTDRATYD YLRSISPDLK IVRGRMDVEA TSLPLMQVVT HGSLRIGFL EGFTLVSEEP DVLLAEANKL DVDVLCWAGG SHRFECFEYM DKFFVNPGSA TGAFTTDWLA EGEEVVPSFC L MDVQGISL TLYVYQLRKD ENGTENVAVE KVTYTKPVEP TGAS

UniProtKB: Vacuolar protein sorting-associated protein 29

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.17 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 71 / Number images used: 18680
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 18680
FSC plot (resolution estimation)

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