[English] 日本語
Yorodumi
- EMDB-50413: Cryo-EM structure of Legionella effector SdeC (3D flexible refinement) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50413
TitleCryo-EM structure of Legionella effector SdeC (3D flexible refinement)
Map data
Sample
  • Complex: SdeC
    • Protein or peptide: SdeC
KeywordsPhospho-ribose ubiquitination / mono-ADP ribosyl transferase / Phosphodiesterase / deubiquitinase / TOXIN
Function / homologySidE, DUB domain / SidE, mono-ADP-ribosyltransferase domain / SidE mono-ADP-ribosyltransferase domain / SidE DUB domain / SidE, PDE domain / SidE phosphodiesterase (PDE) domain / NAD+-protein-arginine ADP-ribosyltransferase activity / protein deubiquitination / SdeC
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsWeng T-H / Misra M / Chen W / Safarian S / Kudryashev M / Dikic I
Funding supportEuropean Union, Germany, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)742720European Union
German Research Foundation (DFG)253130777 Germany
CitationJournal: To Be Published
Title: BAR-like C-terminal domain of Legionella SidE family is crucial for its membrane localization and secretion
Authors: Misra M / Mukherjee R / Bhattacharya A / Chen W / Weng T-H / van Ek L / Cristiani A / Li C / Mohammed A / Liu Y / Pomirska J / Vidov A / Heden van Noort G / Bhaskara R / Svergun D / Gavin AC ...Authors: Misra M / Mukherjee R / Bhattacharya A / Chen W / Weng T-H / van Ek L / Cristiani A / Li C / Mohammed A / Liu Y / Pomirska J / Vidov A / Heden van Noort G / Bhaskara R / Svergun D / Gavin AC / Safarian S / Kudryashev M / Luo Z-Q / Dikic I
History
DepositionMay 24, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50413.png

Downloads & links

-
Map

FileDownload / File: emd_50413.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 301.56 Å		1.08 Å/pix.
x 280 pix.
= 301.56 Å		1.08 Å/pix.
x 280 pix.
= 301.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.077 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0075
Minimum - Maximum-0.027821116 - 0.051419266
Average (Standard dev.)0.00004630286 (±0.0008259448)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 301.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_50413_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_50413_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SdeC

EntireName: SdeC
Components
  • Complex: SdeC
    • Protein or peptide: SdeC

-
Supramolecule #1: SdeC

SupramoleculeName: SdeC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 199 KDa

-
Macromolecule #1: SdeC

MacromoleculeName: SdeC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Legionella pneumophila (bacteria)
Molecular weightTheoretical: 199.470812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM ...String:
MSPILGYWKI KGLVQPTRLL LEYLEEKYEE HLYERDEGDK WRNKKFELGL EFPNLPYYID GDVKLTQSMA IIRYIADKHN MLGGCPKER AEISMLEGAV LDIRYGVSRI AYSKDFETLK VDFLSKLPEM LKMFEDRLCH KTYLNGDHVT HPDFMLYDAL D VVLYMDPM CLDAFPKLVC FKKRIEAIPQ IDKYLKSSKY IAWPLQGWQA TFGGGDHPPK SDLEVLFQGP LGSMPKYVEG VE LTQEGMH AIFARMGHGD ITSGSIYNGV PTIDTEALNR QGFMPVLTGV GPRRDSGHWI MLIKGPGNQY FLFDPLGKTS GEG YKNTLL AQLPIASTLS VIPNEPGLNK GLCGYWVASV GLKARSELSK DNPPNLETLG QITTDAMKDE LTDNGYLKIT GWLK AVADK FPEGDPQPDA KALRQTTEKD LHIEIPSPVS PIKDTAPKEV STKPTAPQVA PKHSLDSKLL ENDDDVLDTI KYVHK EYLG KPYPGPLKNP KAPEEGRLPP NEGPDRGPHG LAHTVRTMAC AEVMIEEARK AQLRGETLGK AKNGQTLADV TPEELK KIL IAQAFFVVGR DDERSGYDDV HKRNFYAEYH EKSEQAFRKY VEDNKLIGKI FKDQKEVDFY AAIILDKNHE WDATPAH IL INQGHMVDLM RTKAPAEVAL ERTYNTLKGT VGSKGAEVVL KAHRDFFFAT GAVVPLVNPE AIDDPSRGGP YENPYSGE K FVIVDDKVPA SKKDLPKAVN RDYKLKDNER FLTIKEYYAF PDVQQTYPGY KTRLEASSYY FPTPFAGECE QNPAKCLGA IQKARSKLQT DAIKNGFQSS SEKERRQPNM DEIAAARIIQ QIMANPDCIH DDHVLINGQK LEEKFFRDLL AKCDMAVVGS LLNDTDIKN IDTLMRHEKN TEFHSTDPKA VPVKIGDAWE NRIRTKGGDV TQMKHDLIFL MQNDAWYFSR VNAIAQNRDK G SNFKEVLF TTLMTPLTNK SLIDTSHVPA PKKLYRGLNL PQEFTNKLIN QSNAIIANTE NTLFTDLSAE AFKQIKLNDF SQ MSGKTCA STTKNMKLLT DIWGSNVIFE MLDPDGLLHP KQVGTHMAGS EDEFSVYLPE DVALVPTKVT LEGKTDTGED RYI FTLVAV KSPDFIPRHE SGYAVEPFMK MQKEKVTQAL DAIEKDKDSY NIDEQLKSLR TEMVRQAKLP LREGVFDRLS HRLS LETSD NKISPERRDF LNQHVIPVLQ ECHIALRAND MDMMQKALAK FPTDKQWSAF KSGEAVRAKA QMDVLKQQIE KKIML QTQI IPALTECGEA LDKQNVTEAL QALNKLPAEK EIGKVKTIGQ ELRGQIVGVK QELTGNLEPL QRATTTPIVQ DAEKIK VRY ETLLTDVTKR VTDFEKIKPA NLDGYNKAIA DLNNIQQELN LLRNEKIRMH TDKDKAVDFS DIEALDKRLQ DVQSKLP TQ LLEQTSKDVA KLAKMPEKIT FNDIKSMTSK MNNYLETLEL IRNDRIKKHA GSTDPLDMSD LDGLKGQLQT YNQSMADI L LRAAKSSLDK IKDPATFEKE SPYIKQCFDH LAELEKTLDD SDKGRKQKED FTAYKSALMD KQEKAYPEML QLQYKSEAL IMQLRDICKI HHDNLAEARR VRLQQLDSQG GGLLGGLWAV TNTIGLTTDN VNIEKMQIRM KEQTLRAFKT ELTNDKLNTD QVIAFLAKG SPSELQEALG ISKENAEQLH GLLKQLEIKT ASTDKLQEIE KLIDEVSTKI GKEPVKQDHT ITIDEEESDD I RYGF

UniProtKB: SdeC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1489769
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Software - details: 3dflex
Details: The final refinement was done using cryoSPARC 3DFlex with an outer solvent mask that includes the whole protein.
Number images used: 149762
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9fgm:
Cryo-EM structure of Legionella effector SdeC (3D flexible refinement)

+
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