[English] 日本語
Yorodumi
- EMDB-19812: Oligomeric structure of SynDLP in presence of GTP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19812
TitleOligomeric structure of SynDLP in presence of GTP
Map data
Sample
  • Cell: filamentous homo-oligomer of SynDLP in presence of GTP
    • Protein or peptide: Slr0869 protein
KeywordsBDLP / cyanobacteria / membrane remodeling / GTPase / 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: 3.6 Å
AuthorsJunglas B / Gewehr L / Schoennenbeck P / Schneider D / Sachse C
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Cell Rep / Year: 2024
Title: Structural basis for GTPase activity and conformational changes of the bacterial dynamin-like protein SynDLP.
Authors: Benedikt Junglas / Lucas Gewehr / Lara Mernberger / Philipp Schönnenbeck / Ruven Jilly / Nadja Hellmann / Dirk Schneider / Carsten Sachse /
Abstract: SynDLP, a dynamin-like protein (DLP) encoded in the cyanobacterium Synechocystis sp. PCC 6803, has recently been identified to be structurally highly similar to eukaryotic dynamins. To elucidate ...SynDLP, a dynamin-like protein (DLP) encoded in the cyanobacterium Synechocystis sp. PCC 6803, has recently been identified to be structurally highly similar to eukaryotic dynamins. To elucidate structural changes during guanosine triphosphate (GTP) hydrolysis, we solved the cryoelectron microscopy (cryo-EM) structures of oligomeric full-length SynDLP after addition of guanosine diphosphate (GDP) at 4.1 Å and GTP at 3.6-Å resolution as well as a GMPPNP-bound dimer structure of a minimal G-domain construct of SynDLP at 3.8-Å resolution. In comparison with what has been seen in the previously resolved apo structure, we found that the G-domain is tilted upward relative to the stalk upon GTP hydrolysis and that the G-domain dimerizes via an additional extended dimerization domain not present in canonical G-domains. When incubated with lipid vesicles, we observed formation of irregular tubular SynDLP assemblies that interact with negatively charged lipids. Here, we provide the structural framework of a series of different functional SynDLP assembly states during GTP turnover.
History
DepositionMar 7, 2024-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19812.png

Downloads & links

-
Map

FileDownload / File: emd_19812.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: 0.159
Minimum - Maximum-0.21886145 - 0.52466905
Average (Standard dev.)0.0024232117 (±0.01959167)
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

-
Sample components

-
Entire : filamentous homo-oligomer of SynDLP in presence of GTP

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

-
Supramolecule #1: filamentous homo-oligomer of SynDLP in presence of GTP

SupramoleculeName: filamentous homo-oligomer of SynDLP in presence of GTP
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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.5 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zw6

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 279572
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
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