[English] 日本語
Yorodumi
- EMDB-43873: Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43873
TitleHuman Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Consensus map)
Map dataPrimary map, unsharpened.
Sample
  • Complex: Trimeric complex of VPS35/VPS29/VPS26 with excess SNX17 peptide
    • Protein or peptide: VPS35 ENDOSOMAL PROTEIN-SORTING FACTOR-LIKE
    • Protein or peptide: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29
    • Protein or peptide: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26C
    • Protein or peptide: Sorting nexin-17
KeywordsRetreiver / CCC / Endosomal recycling / Sorting Nexin / PROTEIN TRANSPORT
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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

-
Structure visualization

Supplemental images

emd_43873.png

Downloads & links

-
Map

FileDownload / File: emd_43873.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary map, unsharpened.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.125
Minimum - Maximum-0.30105925 - 0.6144093
Average (Standard dev.)0.00015280515 (±0.010093902)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half map A.

Fileemd_43873_half_map_1.map
AnnotationHalf map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map B.

Fileemd_43873_half_map_2.map
AnnotationHalf map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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
    • Protein or peptide: VPS35 ENDOSOMAL PROTEIN-SORTING FACTOR-LIKE
    • Protein or peptide: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29
    • Protein or peptide: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26C
    • Protein or peptide: Sorting nexin-17

-
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: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: VPS35 ENDOSOMAL PROTEIN-SORTING FACTOR-LIKE

MacromoleculeName: VPS35 ENDOSOMAL PROTEIN-SORTING FACTOR-LIKE / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPA ALAAAMDSSR RKRDRDDNSV VGSDFEPWTN KRGEILARYT TTEKLSINLF MGSEKGKAGT ATLAMSEKVR T RLEELDDF ...String:
MAVFPWHSRN RNYKAEFASC RLEAVPLEFG DYHPLKPITV TESKTKKVNR KGSTSSTSSS SSSSVVDPLS SVLDGTDPLS MFAATADPA ALAAAMDSSR RKRDRDDNSV VGSDFEPWTN KRGEILARYT TTEKLSINLF MGSEKGKAGT ATLAMSEKVR T RLEELDDF EEGSQKELLN LTQQDYVNRI EELNQSLKDA WASDQKVKAL KIVIQCSKLL SDTSVIQFYP SKFVLITDIL DT FGKLVYE RIFSMCVDSR SVLPDHFSPE NANDTAKETC LNWFFKIASI RELIPRFYVE ASILKCNKFL SKTGISECLP RLT CMIRGI GDPLVSVYAR AYLCRVGMEV APHLKETLNK NFFDFLLTFK QIHGDTVQNQ LVVQGVELPS YLPLYPPAMD WIFQ CISYH APEALLTEMM ERCKKLGNNA LLLNSVMSAF RAEFIATRSM DFIGMIKECD ESGFPKHLLF RSLGLNLALA DPPES DRLQ ILNEAWKVIT KLKNPQDYIN CAEVWVEYTC KHFTKREVNT VLADVIKHMT PDRAFEDSYP QLQLIIKKVI AHFHDF SVL FSVEKFLPFL DMFQKESVRV EVCKCIMDAF IKHQQEPTKD PVILNALLHV CKTMHDSVNA LTLEDEKRML SYLINGF IK MVSFGRDFEQ QLSFYVESRS MFCNLEPVLV QLIHSVNRLA METRKVMKGN HSRKTAAFVR ACVAYCFITI PSLAGIFT R LNLYLHSGQV ALANQCLSQA DAFFKAAISL VPEVPKMINI DGKMRPSESF LLEFLCNFFS TLLIVPDHPE HGVLFLVRE LLNVIQDYTW EDNSDEKIRI YTCVLHLLSA MSQETYLYHI DKVDSNDSLY GGDSKFLAEN NKLCETVMAQ ILEHLKTLAK DEALKRQSS LGLSFFNSIL AHGDLRNNKL NQLSVNLWHL AQRHGCADTR TMVKTLEYIK KQSKQPDMTH LTELALRLPL Q TRT

-
Macromolecule #2: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29

MacromoleculeName: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAGHRLVLVL GDLHIPHRCN SLPAKFKKLL VPGKIQHILC TGNLCTKESY DYLKTLAGDV HIVRGDFDEN LNYPEQKVVT VGQFKIGLI HGHQVIPWGD MASLALLQRQ FDVDILISGH THKFEAFEHE NKFYINPGSA TGAYNALETN IIPSFVLMDI Q ASTVVTYV ...String:
MAGHRLVLVL GDLHIPHRCN SLPAKFKKLL VPGKIQHILC TGNLCTKESY DYLKTLAGDV HIVRGDFDEN LNYPEQKVVT VGQFKIGLI HGHQVIPWGD MASLALLQRQ FDVDILISGH THKFEAFEHE NKFYINPGSA TGAYNALETN IIPSFVLMDI Q ASTVVTYV YQLIGDDVKV ERIEYKKPEN LYFQGGGSGG SHHHHHH

-
Macromolecule #3: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26C

MacromoleculeName: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 26C / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGTALDIKIK RANKVYHAGE VLSGVVVISS KDSVQHQGVS LTMEGTVNLQ LSAKSVGVFE AFYNSVKPIQ IINSTIEMVK PGKFPSGKT EIPFEFPLHL KGNKVLYETY HGVFVNIQYT LRCDMKRSLL AKDLTKTCEF IVHSAPQKGK FTPSPVDFTI T PETLQNVK ...String:
MGTALDIKIK RANKVYHAGE VLSGVVVISS KDSVQHQGVS LTMEGTVNLQ LSAKSVGVFE AFYNSVKPIQ IINSTIEMVK PGKFPSGKT EIPFEFPLHL KGNKVLYETY HGVFVNIQYT LRCDMKRSLL AKDLTKTCEF IVHSAPQKGK FTPSPVDFTI T PETLQNVK ERALLPKFLL RGHLNSTNCV ITQPLTGELV VESSEAAIRS VELQLVRVET CGCAEGYARD ATEIQNIQIA DG DVCRGLS VPIYMVFPRL FTCPTLETTN FKVEFEVNIV VLLHPDHLIT ENFPLKLCRI

-
Macromolecule #4: Sorting nexin-17

MacromoleculeName: Sorting nexin-17 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString:
ASASDVHGNF AFEGIGDEDL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: Non-uniform Refinement / 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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more