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- PDB-23at: Structure of Arabidopsis SNX1 (Class ll, 6-fold) -

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Basic information

Entry
Database: PDB / ID: 23at
TitleStructure of Arabidopsis SNX1 (Class ll, 6-fold)
ComponentsSorting nexin 1
KeywordsMEMBRANE PROTEIN / SNX protein / Arabidopsis thaliana / tube
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsLi, Y.B. / Tao, R. / Zhang, H. / Wen, X.K. / Leung, S.K.P. / Lau, W.C.Y. / Jiang, L.W. / Cui, Y.
Funding support China, Hong Kong, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32270727, 32000141 China
Other government2021J01029
Other government20720210094 China
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, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: Sorting nexin 1
1: Sorting nexin 1
2: Sorting nexin 1
3: Sorting nexin 1
4: Sorting nexin 1
5: Sorting nexin 1
6: Sorting nexin 1
7: Sorting nexin 1
8: Sorting nexin 1
9: Sorting nexin 1
A: Sorting nexin 1
AA: Sorting nexin 1
AB: Sorting nexin 1
B: Sorting nexin 1
C: Sorting nexin 1
D: Sorting nexin 1
E: Sorting nexin 1
F: Sorting nexin 1
G: Sorting nexin 1
H: Sorting nexin 1
I: Sorting nexin 1
J: Sorting nexin 1
K: Sorting nexin 1
L: Sorting nexin 1
M: Sorting nexin 1
N: Sorting nexin 1
O: Sorting nexin 1
P: Sorting nexin 1
Q: Sorting nexin 1
R: Sorting nexin 1
S: Sorting nexin 1
T: Sorting nexin 1
U: Sorting nexin 1
V: Sorting nexin 1
W: Sorting nexin 1
X: Sorting nexin 1
Y: Sorting nexin 1
Z: Sorting nexin 1
a: Sorting nexin 1
b: Sorting nexin 1
c: Sorting nexin 1
d: Sorting nexin 1
e: Sorting nexin 1
f: Sorting nexin 1
g: Sorting nexin 1
h: Sorting nexin 1
i: Sorting nexin 1
j: Sorting nexin 1
k: Sorting nexin 1
l: Sorting nexin 1
m: Sorting nexin 1
n: Sorting nexin 1
o: Sorting nexin 1
p: Sorting nexin 1
q: Sorting nexin 1
r: Sorting nexin 1
s: Sorting nexin 1
t: Sorting nexin 1
u: Sorting nexin 1
v: Sorting nexin 1
w: Sorting nexin 1
x: Sorting nexin 1
y: Sorting nexin 1
z: Sorting nexin 1


Theoretical massNumber of molelcules
Total (without water)2,982,02464
Polymers2,982,02464
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Sorting nexin 1 / AtSNX1 / Vacuolar protein sorting-associated protein 5 homolog


Mass: 46594.121 Da / Num. of mol.: 64
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SNX1, VPS5, At5g06140, K16F4.11, MBL20 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9FG38
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Arabidopsis thaliana SNX1 complex with liposome / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -60.3 ° / Axial rise/subunit: 9.55 Å / Axial symmetry: C1
3D reconstructionResolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20728 / Symmetry type: HELICAL

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