[English] 日本語
Yorodumi
- EMDB-68806: Structure of Arabidopsis SNX1 (Class ll, 6-fold) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-68806
TitleStructure of Arabidopsis SNX1 (Class ll, 6-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: 8.7 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 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 YB / Tao R / Zhang H / Wen XK / Leung SKP / Qi Q / Zheng XH / Guo HX / Wu CX / Fu ZF / Huang XR / Sun MX / Lau WCY / Jiang LW / Cui Y
History
DepositionJan 30, 2026-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_68806.png

Downloads & links

-
Map

FileDownload / File: emd_68806.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.10000932 - 0.25375223
Average (Standard dev.)0.00039176713 (±0.024135338)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_68806_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_68806_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
Macromolecule #1: Sorting nexin 1

MacromoleculeName: Sorting nexin 1 / type: protein_or_peptide / ID: 1 / Number of copies: 64 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

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

-
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

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.55 Å
Applied symmetry - Helical parameters - Δ&Phi: -60.3 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 20728
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE
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