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- PDB-9glc: NONO/SFPQ filament: local refinement central units (strand 1) -

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Basic information

Entry
Database: PDB / ID: 9glc
TitleNONO/SFPQ filament: local refinement central units (strand 1)
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
BC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BD: Non-POU domain containing octamer binding
BE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BF: Non-POU domain containing octamer binding
AC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AD: Non-POU domain containing octamer binding
AE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CF: Non-POU domain containing octamer binding


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

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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

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Experimental details

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Experiment

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

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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

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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

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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_d0.00514640
ELECTRON MICROSCOPYf_angle_d0.70719577
ELECTRON MICROSCOPYf_dihedral_angle_d4.2121944
ELECTRON MICROSCOPYf_chiral_restr0.0431991
ELECTRON MICROSCOPYf_plane_restr0.0052679

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