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- EMDB-68805: Structure of Arabidopsis SNX1 (Class l, 7-fold) -

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Basic information

Entry
Database: EMDB / ID: EMD-68805
TitleStructure of Arabidopsis SNX1 (Class l, 7-fold)
Map data
Sample
  • Complex: Arabidopsis thaliana SNX1 complex with liposome
    • Protein or peptide: Sorting nexin 1
KeywordsSNX protein / Arabidopsis thaliana / tube / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive gravitropism / root development / Golgi to vacuole transport / retromer complex / protein targeting to vacuole / endosome to lysosome transport / multivesicular body / phosphatidylinositol binding / protein localization to plasma membrane / endosome ...positive gravitropism / root development / Golgi to vacuole transport / retromer complex / protein targeting to vacuole / endosome to lysosome transport / multivesicular body / phosphatidylinositol binding / protein localization to plasma membrane / endosome / endosome membrane / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
Methodhelical reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsLi YB / Tao R / Zhang H / Wen XK / Leung SKP / Lau WCY / Jiang LW / Cui Y
Funding support China, Hong Kong, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270727, 32000141 China
Other government2021J01029
Other government20720210094
The University Grants Committee, Research Grants Council (RGC)CUHK14106823, C4033-19E, C4002-20W, C4002-21EF, C4014-23G, R4005-18, Senior Research Fellow Scheme SRFS2122-4S01 and CRS_CUHK405/23 Hong Kong
CitationJournal: Nat Commun / Year: 2026
Title: SNX-mediated biogenesis of a plant-unique vesicle derived from the multivesicular body.
Authors: Yanbin Li / Ran Tao / Hai Zhang / Xiaokang Wen / Stephen King Pong Leung / Qing Qi / Xiaohui Zheng / Haoxuan Guo / Congxian Wu / Zhifei Fu / Xiaorong Huang / Wilson Chun Yu Lau / Liwen Jiang / Yong Cui /
Abstract: Retrograde transport is central to endomembrane homeostasis, yet the identity and origin of plant retrograde carriers remain unresolved. Prevailing models propose that plant vacuolar sorting ...Retrograde transport is central to endomembrane homeostasis, yet the identity and origin of plant retrograde carriers remain unresolved. Prevailing models propose that plant vacuolar sorting receptors (VSRs) recycle either from multivesicular bodies (MVBs) to the trans-Golgi network (TGN) or from the TGN to the Golgi apparatus and/or endoplasmic reticulum (ER). However, the ultrastructural features of plant retrograde transport carriers remain largely unresolved. Here, we show that plant retrograde transport is likely mediated by a previously unrecognized class of MVB-derived spherical vesicles. Using correlative light and electron microscopy and three-dimensional electron tomography, we identify a distinct population of ~30-50 nm spherical vesicles adjacent to MVBs, including nascent vesicles budding from the MVB limiting membrane in Arabidopsis root cells. Immunogold labeling shows that these vesicles are enriched in retromer components and VSRs, suggesting that they possibly function as retrograde transport carriers. To investigate their biogenesis, we perform cryo-electron microscopy and liposome tubulation assays, showing that Arabidopsis SNX1 generates shorter membrane tubules than its mammalian counterpart, consistent with reduced membrane affinity linked to differences in the amphipathic helix. Notably, the SNX1-SNX2 heterodimer produces heterogeneous structures, including spherical vesicles, recapitulating in vivo observations. Lastly, knockdown of SNX1 or SNX2 results in vacuolar mislocalization and increased degradation of GFP-VSR2, and defects in SNX1 and VPS29 inhibit formation of spherical vesicles adjacent to MVBs, resulting in embryonic lethality before the globular stage. Together, these findings establish MVB-derived spherical vesicles as plant retrograde carriers and reveal a distinct SNX-mediated mechanism underlying their formation.
History
DepositionJan 30, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68805.png

Downloads & links

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Map

FileDownload / File: emd_68805.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.84 Å/pix.
x 400 pix.
= 736. Å		1.84 Å/pix.
x 400 pix.
= 736. Å		1.84 Å/pix.
x 400 pix.
= 736. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.095647454 - 0.30510113
Average (Standard dev.)0.00091110956 (±0.031921208)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 736.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68805_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68805_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Arabidopsis thaliana SNX1 complex with liposome

EntireName: Arabidopsis thaliana SNX1 complex with liposome
Components
  • Complex: Arabidopsis thaliana SNX1 complex with liposome
    • Protein or peptide: Sorting nexin 1

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Supramolecule #1: Arabidopsis thaliana SNX1 complex with liposome

SupramoleculeName: Arabidopsis thaliana SNX1 complex with liposome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Sorting nexin 1

MacromoleculeName: Sorting nexin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 81 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 46.594121 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MESTEQPRNI SGSMQSPRSP SSHPYLSVSV TDPVKLGNGV QAYISYRVIT KTNLPEYQGP EKIVIRRYSD FVWLRDRLFE KYKGIFIPP LPEKSAVEKF RFSAEFIEMR RAALDIFVNR IALHPELQQS EDLRTFLQAD EETMDRFRFQ ETSIFKKPAD L MQMFRDVQ ...String:
MESTEQPRNI SGSMQSPRSP SSHPYLSVSV TDPVKLGNGV QAYISYRVIT KTNLPEYQGP EKIVIRRYSD FVWLRDRLFE KYKGIFIPP LPEKSAVEKF RFSAEFIEMR RAALDIFVNR IALHPELQQS EDLRTFLQAD EETMDRFRFQ ETSIFKKPAD L MQMFRDVQ SKVSDAVLGK EKPVEETTAD YEKLKHYIFE LENHLTEAQK HAYRLVKRHR ELGQSLLDFG KAVKLLGACE GE PTGKAFS DLGTKSELLS IKLQKEAQQV LMNFEEPLKD YVRYVQSIKA TIAERGTAFK QHCELSETTK LKEINLDKLM LTR SDKVGE AEIEYREIKA ESEEATRRFE RIVKRMEDEI VRFQEQKTEE MGVAFHQFAK GQARLANSVA DAWRSLLPKL EASY SV

UniProtKB: Sorting nexin 1

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.18 Å
Applied symmetry - Helical parameters - Δ&Phi: -51.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49380
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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