[English] 日本語
Yorodumi
- PDB-9slf: Open conformation dome complex including the Sec-translocon (SecY... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9slf
TitleOpen conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Components
  • (Uncharacterized lipoprotein ...) x 3
  • Probable protein-export membrane protein SecG
  • Protein translocase subunit SecY
  • SecDF
  • SecE
KeywordsTRANSLOCASE / in-cell cryo-ET / Protein Folding / cell surface / Translocation / Sec-machinery
Function / homology
Function and homology information


intracellular protein transmembrane transport / protein transport by the Sec complex / protein-transporting ATPase activity / protein secretion / transmembrane protein transporter activity / protein targeting / membrane / plasma membrane
Similarity search - Function
Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecY / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site ...Protein of unknown function DUF3713 / Protein of unknown function (DUF3713) / Preprotein translocase SecG subunit / SecE subunit of protein translocation complex, bacterial-like / Protein translocase subunit SecY / Protein secY signature 1. / Protein secY signature 2. / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Uncharacterized protein MG055 homolog / Uncharacterized lipoprotein MG338 homolog / Uncharacterized lipoprotein MG309 homolog / Uncharacterized lipoprotein MG307 homolog / Uncharacterized protein MG277 homolog / Protein translocase subunit SecY / Probable protein-export membrane protein SecG
Similarity search - Component
Biological speciesMycoplasmoides pneumoniae M129 (bacteria)
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 17 Å
AuthorsJensen, R.K. / Xue, L. / Mahamid, J.
Funding support Denmark, United States, 2items
OrganizationGrant numberCountry
Danish Council for Independent Research0106-00010A Denmark
Chan Zuckerberg Initiative2021-234620 United States
CitationJournal: To Be Published
Title: In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex
Authors: Jensen, R.K. / Xue, L. / Marotta, F. / Somody, J.C. / Selkrig, J. / Lenz, S. / Rappsilber, J. / Savitski, M.M. / Kosinski, J. / Typas, A. / Zimmermann-Kogadeeva, M. / Bork, P. / Mahamid, J.
History
DepositionSep 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
D: SecDF
E: SecE
G: Probable protein-export membrane protein SecG
Y: Protein translocase subunit SecY
C: Uncharacterized lipoprotein MG309 homolog
F: Uncharacterized lipoprotein MG338 homolog
B: Uncharacterized lipoprotein MG307 homolog


Theoretical massNumber of molelcules
Total (without water)603,2217
Polymers603,2217
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Protein , 4 types, 4 molecules DEGY

#1: Protein SecDF


Mass: 108345.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75387
#2: Protein SecE


Mass: 14489.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75048
#3: Protein Probable protein-export membrane protein SecG


Mass: 8352.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q9EXD0
#4: Protein Protein translocase subunit SecY


Mass: 52003.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: Q59548

-
Uncharacterized lipoprotein ... , 3 types, 3 molecules CFB

#5: Protein Uncharacterized lipoprotein MG309 homolog


Mass: 143385.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75334
#6: Protein Uncharacterized lipoprotein MG338 homolog


Mass: 140427.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75296
#7: Protein Uncharacterized lipoprotein MG307 homolog


Mass: 136216.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycoplasmoides pneumoniae M129 (bacteria) / References: UniProt: P75342

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: subtomogram averaging

-
Sample preparation

ComponentName: Open conformation dome complex including the Sec-translocon (SecYEG-SecA-SecDF) in untreated Mycoplasma pneumoniae cells
Type: CELL / Entity ID: all / Source: NATURAL
Source (natural)Organism: Mycoplasmoides pneumoniae M129 (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 2.9 e/Å2 / Avg electron dose per subtomogram: 115 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1Warp1.0.9volume selection
4Warp1.0.9CTF correction
7PowerFitmodel fitting
8UCSF ChimeraXmodel fitting
12RELION4.0.1final Euler assignment
14RELION4.0.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 17 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1001 / Symmetry type: POINT
EM volume selectionMethod: Manual picking and Deep-learning based particle picking
Details: Initial particles were manually picked and used to generate training data for iterative rounds of DeePiCt particle picking and junk cleaning with 3D classification in RELION. A final round ...Details: Initial particles were manually picked and used to generate training data for iterative rounds of DeePiCt particle picking and junk cleaning with 3D classification in RELION. A final round of multi-class particle picking was performed in DeepFinder followed by manual curation of the final particle positions.
Num. of tomograms: 183 / Num. of volumes extracted: 6103 / Reference model: Data-driven, Iteratively improved
Atomic model buildingProtocol: RIGID BODY FIT
Details: Initial fitting with PowerFit into the map of the closed conformation of the complex (EMD-54986). The closed conformation (PDB: 9SLC) was rigid body fitted into the open conformation of the ...Details: Initial fitting with PowerFit into the map of the closed conformation of the complex (EMD-54986). The closed conformation (PDB: 9SLC) was rigid body fitted into the open conformation of the map, and the AlphaFold3 multimer prediction of subcomplex SecYEG-DF was aligned to and replaced the old AlphaFold2 models of these proteins. The SecYEG-DF subcomplex as well as the remaining proteins were each rigid body fitted as single rigid bodies using ChimeraX fit-to-map.
Atomic model buildingSource name: AlphaFold / Type: in silico model

+
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