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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: To Be Published
Title: Plant unique recycling endosomes are derived from multivesicular bodies
Authors: Li, Y.B. / Tao, R. / Zhang, H. / Wen, X.K. / Leung, S.K.P. / Qi, Q. / Zheng, X.H. / Guo, H.X. / Wu, C.X. / Fu, Z.F. / Huang, X.R. / Sun, M.X. / Lau, W.C.Y. / Jiang, L.W. / Cui, Y.
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
Revision 1.0Mar 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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