[English] 日本語
Yorodumi
- PDB-9gld: NONO/SFPQ filament: local refinement central units (strand 2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gld
TitleNONO/SFPQ filament: local refinement central units (strand 2)
Components
  • Non-POU domain containing octamer binding
  • Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
KeywordsNUCLEAR PROTEIN / filament / RNA binding / DNA binding / gene regulation
Function / homology
Function and homology information


dendritic transport of messenger ribonucleoprotein complex / positive regulation of sister chromatid cohesion / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / paraspeckles / chromosome organization / activation of innate immune response / double-strand break repair via homologous recombination ...dendritic transport of messenger ribonucleoprotein complex / positive regulation of sister chromatid cohesion / negative regulation of circadian rhythm / alternative mRNA splicing, via spliceosome / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / paraspeckles / chromosome organization / activation of innate immune response / double-strand break repair via homologous recombination / regulation of circadian rhythm / RNA polymerase II transcription regulator complex / histone deacetylase binding / nuclear matrix / fibrillar center / transcription cis-regulatory region binding / nuclear speck / chromatin remodeling / innate immune response / negative regulation of DNA-templated transcription / dendrite / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / RNA binding / identical protein binding
Similarity search - Function
p54nrb, RNA recognition motif 1 / PSF, RNA recognition motif 1 / PSF, NOPS domain / NOPS / NOPS (NUC059) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Non-POU domain-containing octamer-binding protein / Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
Similarity search - Component
Biological speciesCricetulus griseus (Chinese hamster)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRasmussen, T. / Bottcher, B.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
CitationJournal: to be published
Title: A filamentous scaffold for gene regulation
Authors: Rasmussen, T. / Kuspert, J. / Schonemann, L. / Geiger, D. / Bottcher, B.
History
DepositionAug 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 10, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
BA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BB: Non-POU domain containing octamer binding
BG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BH: Non-POU domain containing octamer binding
AA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AB: Non-POU domain containing octamer binding
AG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AH: Non-POU domain containing octamer binding
CG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
DA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)


Theoretical massNumber of molelcules
Total (without water)673,36010
Polymers673,36010
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein
Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)


Mass: 75880.156 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A8C2LX33
#2: Protein
Non-POU domain containing octamer binding / Non-POU domain-containing octamer-binding protein isoform X2


Mass: 54519.828 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A8C2L8F1
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: NONO/SFPQ filament / Type: COMPLEX / Details: filaments formed by concentrating to 1 mg/ml / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
35 mMEDTAC10H16N2O81
40.03 %DDMC24H46O111
510 mMmagnesium chlorideMgCl21
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: blot time 5 sec, blot force +20

-
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 magnification: 130000 X / Nominal defocus max: 1400 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 6.2 sec. / Electron dose: 70 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 17059
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 5 eV

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4144650 / Details: blob picker
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2974535 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: first rigid fitting with Chimera, then further refinemnt with Coot, C-terminal some de-novo residues
Atomic model building

3D fitting-ID: 1 / Accession code: 6WMZ / Initial refinement model-ID: 1 / PDB-ID: 6WMZ

6wmz

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-IDChain residue rangeDetailsPdb chain residue range
1AA367-589SFPQ367-589
2BB148-307NONO148-307
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00814850
ELECTRON MICROSCOPYf_angle_d0.78719856
ELECTRON MICROSCOPYf_dihedral_angle_d3.8511974
ELECTRON MICROSCOPYf_chiral_restr0.0412017
ELECTRON MICROSCOPYf_plane_restr0.0052714

+
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