[English] 日本語
Yorodumi
- EMDB-14993: Oligomeric structure of SynDLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14993
TitleOligomeric structure of SynDLP
Map data
Sample
  • Cell: filamentous homo-oligomer of SynDLP
    • Protein or peptide: Slr0869 protein
KeywordsBDLP / cyanobacteria / membrane remodeling / LIPID BINDING PROTEIN
Function / homologyMitofusin family / Dynamin, N-terminal / Dynamin family / GTPase activity / P-loop containing nucleoside triphosphate hydrolase / Slr0869 protein
Function and homology information
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGewehr L / Junglas B / Jilly R / Franz J / Wenyu EZ / Weidner T / Bonn M / Sachse C / Schneider D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Nat Commun / Year: 2023
Title: SynDLP is a dynamin-like protein of Synechocystis sp. PCC 6803 with eukaryotic features.
Authors: Lucas Gewehr / Benedikt Junglas / Ruven Jilly / Johannes Franz / Wenyu Eva Zhu / Tobias Weidner / Mischa Bonn / Carsten Sachse / Dirk Schneider /
Abstract: Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin- ...Dynamin-like proteins are membrane remodeling GTPases with well-understood functions in eukaryotic cells. However, bacterial dynamin-like proteins are still poorly investigated. SynDLP, the dynamin-like protein of the cyanobacterium Synechocystis sp. PCC 6803, forms ordered oligomers in solution. The 3.7 Å resolution cryo-EM structure of SynDLP oligomers reveals the presence of oligomeric stalk interfaces typical for eukaryotic dynamin-like proteins. The bundle signaling element domain shows distinct features, such as an intramolecular disulfide bridge that affects the GTPase activity, or an expanded intermolecular interface with the GTPase domain. In addition to typical GD-GD contacts, such atypical GTPase domain interfaces might be a GTPase activity regulating tool in oligomerized SynDLP. Furthermore, we show that SynDLP interacts with and intercalates into membranes containing negatively charged thylakoid membrane lipids independent of nucleotides. The structural characteristics of SynDLP oligomers suggest it to be the closest known bacterial ancestor of eukaryotic dynamin.
History
DepositionMay 18, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14993.png

Downloads & links

-
Map

FileDownload / File: emd_14993.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 450 pix.
= 391.05 Å		0.87 Å/pix.
x 450 pix.
= 391.05 Å		0.87 Å/pix.
x 450 pix.
= 391.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.869 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.4036487 - 0.7791832
Average (Standard dev.)0.0024141194 (±0.02117513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 391.05002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14993_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_14993_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14993_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : filamentous homo-oligomer of SynDLP

EntireName: filamentous homo-oligomer of SynDLP
Components
  • Cell: filamentous homo-oligomer of SynDLP
    • Protein or peptide: Slr0869 protein

-
Supramolecule #1: filamentous homo-oligomer of SynDLP

SupramoleculeName: filamentous homo-oligomer of SynDLP / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

-
Macromolecule #1: Slr0869 protein

MacromoleculeName: Slr0869 protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 93.705398 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKIAPQCQN LREQVNQLIE LLRQEPTLRS QQDTSIVETA LGKALSPRFE IVFAGAFSAG KSMLINALLE RELLYSAEGH ATGTECHIE YANANEERVV LTFLSEAEIR QQALILAKYL NVNVGDLNIN QPEAVKVVSQ YCQKIIAEEG GENKSERAKQ A NALHLLLI ...String:
MSKIAPQCQN LREQVNQLIE LLRQEPTLRS QQDTSIVETA LGKALSPRFE IVFAGAFSAG KSMLINALLE RELLYSAEGH ATGTECHIE YANANEERVV LTFLSEAEIR QQALILAKYL NVNVGDLNIN QPEAVKVVSQ YCQKIIAEEG GENKSERAKQ A NALHLLLI GFEQNRERIN TVQNSTYSMD QLNFSSLAEA AGYARRGANS AVLKRLDYFC NHSLLKDGNV LVDLPGIDAP VK EDAERAY RKIESPDTSA VICVLKPAAA GDMSAEETQL LERISKNHGI RDRVFYVFNR IDDTWYNTQL RQRLEGLIQS QFR DNSRVY KTSGLLGFYG SQVKQTNSST RFGLDSIFAT TIKGFDGEEE TPQFVSEFNN YCANSGKLLS TAFRVSVNGY ETSN ENYVR ILSEWGIPLV DQLIHDSGIE SFRSGIGLYL AEEKYPELFA TLANDLQPLC IALRQFYLEN YRQLDSQPRE IAAMK AQEL TLLNQEMQNL GIEFKKYMSA QINDVVIGND REFDQDFTKL KARMVARLDE LLKTFSVMNA YKRATESHPR NSTAPF IAV LVEALYYLAN ELEDAFIEAI HELVKNFFQR LGDRLRKVDC YHQVYRLVGN DGGIEQLLRR AEEDITKALV NEARTEC DR YVRESPRFYD EGTFSIYQFR QTLQQTSQGY DAQAIVEAEP AIKELLKLDF EPKVFNTVRK NFRQTVNNTL KTHLLPMA E EQAQIILEQY DVARKYREQT LEQDAEEKIA RNSRLQSEIK QKIDLYQTSI VSINECLKAM QIFEQLPVIT ESDITKQAE IVADADFVEI VELEHHHHHH

UniProtKB: Slr0869 protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.0 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
5.0 mMMgCl2magnesium chloride
7.5 mMKClpotassium chloride
20.0 mMHEPESHEPES
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting force -10 Blotting time 3 s.

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 8322 / Average exposure time: 2.0 sec. / Average electron dose: 26.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 49000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 977199
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7zw6:
Oligomeric structure of SynDLP

+
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