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- PDB-9gni: NONO/SFPQ filament: composite structure -

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Basic information

Entry
Database: PDB / ID: 9gni
TitleNONO/SFPQ filament: composite structure
Components
  • Non-POU domain-containing octamer-binding protein isoform X2
  • 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: 3.9 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
DepositionSep 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 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
AA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AB: Non-POU domain-containing octamer-binding protein isoform X2
AC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AD: Non-POU domain-containing octamer-binding protein isoform X2
AE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AF: Non-POU domain-containing octamer-binding protein isoform X2
AG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
AH: Non-POU domain-containing octamer-binding protein isoform X2
BA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BB: Non-POU domain-containing octamer-binding protein isoform X2
BC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BD: Non-POU domain-containing octamer-binding protein isoform X2
BE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BF: Non-POU domain-containing octamer-binding protein isoform X2
BG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
BH: Non-POU domain-containing octamer-binding protein isoform X2
CA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CB: Non-POU domain-containing octamer-binding protein isoform X2
CC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CD: Non-POU domain-containing octamer-binding protein isoform X2
CE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CF: Non-POU domain-containing octamer-binding protein isoform X2
CG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
CH: Non-POU domain-containing octamer-binding protein isoform X2
DA: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
DB: Non-POU domain-containing octamer-binding protein isoform X2
DC: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
DD: Non-POU domain-containing octamer-binding protein isoform X2
DG: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
DH: Non-POU domain-containing octamer-binding protein isoform X2
DE: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
DF: Non-POU domain-containing octamer-binding protein isoform X2


Theoretical massNumber of molelcules
Total (without water)2,086,40032
Polymers2,086,40032
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.: 16 / Source method: isolated from a natural source / Source: (natural) Cricetulus griseus (Chinese hamster) / References: UniProt: A0A8C2LX33
#2: Protein
Non-POU domain-containing octamer-binding protein isoform X2 / Non-POU-domain-containing / octamer binding protein


Mass: 54519.828 Da / Num. of mol.: 16 / 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 / 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
Details: filaments were obtained by concentrating the sample to 1 mg/ml
Specimen supportGrid material: GOLD / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: 5 sec blotting time, +20 blot force

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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: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2974535 / Algorithm: FOURIER SPACE
Details: This is a composite map produced with Phenix "combine focused maps" (1.20.1) with EMD-51413 (overall consensus map), EMD-51417 and EMD-51418 (focused maps of single strands), EMD-51438 and ...Details: This is a composite map produced with Phenix "combine focused maps" (1.20.1) with EMD-51413 (overall consensus map), EMD-51417 and EMD-51418 (focused maps of single strands), EMD-51438 and EMD-51439 (focused maps of central units from single strands)
Symmetry type: POINT
Atomic model buildingB value: 150 / Protocol: FLEXIBLE FIT / Space: REAL
Details: initially the crystal strucutre model of the heterodimer (PDB 6WMZ) was used for rigid fitting for the focused maps and further refined. The complete dimers of the focused models (PDB 9GLC ...Details: initially the crystal strucutre model of the heterodimer (PDB 6WMZ) was used for rigid fitting for the focused maps and further refined. The complete dimers of the focused models (PDB 9GLC and 9GLD) were used as templates for 4 repeats of the filament in the composite map (also containing the RRM1 domains by rigid fitting) to represent the biological assembly.
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDDetailsInitial refinement model-ID
16WMZ

6wmz

A6WMZASFPQ1
26WMZ

6wmz

B6WMZBNONO1
39GLC

9glc

BC9GLCBCSFPQ2
49GLC

9glc

BE9GLCBESFPQ2
59GLC

9glc

BD9GLCBDNONO2
69GLC

9glc

BF9GLCBFNONO2
79GLD

9gld

AA9GLDAASFPQ3
89GLD

9gld

BG9GLDBGSFPQ3
99GLD

9gld

AB9GLDABNONO3
109GLD

9gld

BH9GLDBHNONO3
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00375766
ELECTRON MICROSCOPYf_angle_d0.577101408
ELECTRON MICROSCOPYf_dihedral_angle_d3.68410110
ELECTRON MICROSCOPYf_chiral_restr0.03910456
ELECTRON MICROSCOPYf_plane_restr0.00413669

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