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- EMDB-43870: Local refined map of VPS35L(partial)-VPS26C-SNX17 -

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Basic information

Entry
Database: EMDB / ID: EMD-43870
TitleLocal refined map of VPS35L(partial)-VPS26C-SNX17
Map dataMain map
Sample
  • Complex: Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide
KeywordsRetreiver / CCC / Endosomal recycling / Sorting Nexin / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsChen B / Chen Z / Han Y / Boesch DJ / Juneja P / Burstein E / Fung HYJ
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128786 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK107733 United States
National Science Foundation (NSF, United States)2047640 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for Retriever-SNX17 assembly and endosomal sorting.
Authors: Amika Singla / Daniel J Boesch / Ho Yee Joyce Fung / Chigozie Ngoka / Avery S Enriquez / Ran Song / Daniel A Kramer / Yan Han / Esther Banarer / Andrew Lemoff / Puneet Juneja / Daniel D ...Authors: Amika Singla / Daniel J Boesch / Ho Yee Joyce Fung / Chigozie Ngoka / Avery S Enriquez / Ran Song / Daniel A Kramer / Yan Han / Esther Banarer / Andrew Lemoff / Puneet Juneja / Daniel D Billadeau / Xiaochen Bai / Zhe Chen / Emre E Turer / Ezra Burstein / Baoyu Chen /
Abstract: During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms ...During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms underlying this interaction have remained elusive. Here, we provide biochemical, structural, cellular, and proteomic analyses of the SNX17-Retriever interaction. Our data reveal that SNX17 adopts an autoinhibited conformation in the basal state, with its FERM domain sequestering its C-terminal tail. The binding of cargo proteins to the FERM domain displaces the C-terminal tail through direct competition. The released tail engages with Retriever by binding to a highly conserved interface between its VPS35L and VPS26C subunits, as revealed by cryogenic electron microscopy (cryo-EM). Disrupting this interface impairs the Retriever-SNX17 interaction, subsequently affecting the recycling of SNX17-dependent cargoes and altering the composition of the plasma membrane proteome. Intriguingly, the SNX17-binding pocket on Retriever can be utilized by other ligands containing a consensus acidic C-terminal tail motif. Together, our findings uncover a mechanism underlying endosomal trafficking of critical cargo proteins and reveal how Retriever can potentially engage with other regulatory factors or be exploited by pathogens.
History
DepositionFeb 28, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateDec 11, 2024-
Current statusDec 11, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43870.png

Downloads & links

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Map

FileDownload / File: emd_43870.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 330.64 Å		1.03 Å/pix.
x 320 pix.
= 330.64 Å		1.03 Å/pix.
x 320 pix.
= 330.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.27687904 - 0.63654095
Average (Standard dev.)0.00033544944 (±0.009098206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 330.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_43870_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_43870_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide

EntireName: Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide
Components
  • Complex: Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide

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Supramolecule #1: Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide

SupramoleculeName: Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1009886 / Details: Blob picking in cryoSPARC Live
Startup modelType of model: INSILICO MODEL
In silico model: 559719 particles after 2D classification, further classified into 3 classes obtained using ab initio reconstruction.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: Non-uniform Refinement
Details: Local refined map of the whole particle stack used to generate the consensus volume in the masked region containing VPS26C- and SNX17-bound half of VPS35L.
Number images used: 227973
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC / Software - details: Heterogenous Refinement
FSC plot (resolution estimation)

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