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- EMDB-51438: NONO/SFPQ filament: local refinement central units (strand 1) -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51438
TitleNONO/SFPQ filament: local refinement central units (strand 1)
Map datalocal refinement, sharpened with Phenix-autosharpen B = 50
Sample
  • Complex: NONO/SFPQ filament
    • Protein or peptide: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
    • Protein or peptide: Non-POU domain containing octamer binding
Keywordsfilament / RNA binding / DNA binding / gene regulation / NUCLEAR PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsRasmussen T / Bottcher B
Funding support Germany, 3 items
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, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51438.png

Downloads & links

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Map

FileDownload / File: emd_51438.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement, sharpened with Phenix-autosharpen B = 50
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å		0.95 Å/pix.
x 512 pix.
= 484.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-78.176413999999994 - 122.228250000000003
Average (Standard dev.)-0.00000000000093 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 484.352 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51438_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_51438_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_51438_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NONO/SFPQ filament

EntireName: NONO/SFPQ filament
Components
  • Complex: NONO/SFPQ filament
    • Protein or peptide: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
    • Protein or peptide: Non-POU domain containing octamer binding

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Supramolecule #1: NONO/SFPQ filament

SupramoleculeName: NONO/SFPQ filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: filaments formed by concentrating to 1 mg/ml
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Macromolecule #1: Splicing factor proline/glutamine rich (polypyrimidine tract bind...

MacromoleculeName: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 75.880156 KDa
SequenceString: MSRDRFRSRG GGGGGFHRRG GGGGRGGLHD FRSPPPGMGL NQNRGPMGPG PGGPKPPIPP PPPHQQQPQQ PPPQQPPPQQ PPPHQQPPP HQPPHQQPPP PPQDSSKPVV PQGPGSAPGV SPAPPPAGSA PPANPPTTGA PPGPGPTPTP PPAVTSATPG P PPPSTPSS ...String:
MSRDRFRSRG GGGGGFHRRG GGGGRGGLHD FRSPPPGMGL NQNRGPMGPG PGGPKPPIPP PPPHQQQPQQ PPPQQPPPQQ PPPHQQPPP HQPPHQQPPP PPQDSSKPVV PQGPGSAPGV SPAPPPAGSA PPANPPTTGA PPGPGPTPTP PPAVTSATPG P PPPSTPSS GVSTTPPQSG GPPPPPAGGA GPGPKQGPGP GPGGPKGGKM PGGPKPGGGP GMGAPGGHPK PPHRGGGEPR GG RQHHPPY HQQHHQGPPP GGPAARTEEK ISDSEGFKAN LSLLRRPGEK TYTQRCRLFV GNLPADITED EFKRLFAKYG EPG EVFINK GKGFGFIKLE SRALAEIAKA ELDDTPMRGR QLRVRFATHA AALSVRNLSP YVSNELLEEA FSQFGPIERA VVIV DDRGR STGKGIVEFA SKPAARKAFE RCSEGVFLLT TTPRPVIVEP LEQLDDEDGL PEKLAQKNPM YQKERETPPR FAQHG TFEY EYSQRWKSLD EMEKQQREQV EKNMKDAKDK LESEMEDAYH EHQANLLRQD LMRRQEELRR MEELHSQEMQ KRKEMQ LRQ EEERRRREEE MMIRQREMEE QMRRQREESY SRMGYMDPRE RDMRMGGGGT MNMGDPYGSG GQKFPPLGGG GGIGYEA NP GVPPATMSGS MMGSDMRTER FGQGGAGPVG GQGPRGMGPG TPAGYGRGRE EYEGPNKKPR F

UniProtKB: Splicing factor proline/glutamine rich (polypyrimidine tract binding protein associated)

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Macromolecule #2: Non-POU domain containing octamer binding

MacromoleculeName: Non-POU domain containing octamer binding / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
Molecular weightTheoretical: 54.519828 KDa
SequenceString: MQSNKTFNLE KQNHTPRKHH QHHHQQHHQQ QQQQQQQPPP PIPANGQQAS SQNEGLTIDL KNFRKPGEKT FTQRSRLFVG NLPPDITEE EMRKLFEKYG KAGEVFIHKD KGFGFIRLET RTLAEIAKVE LDNMPLRGKQ LRVRFACHSA SLTVRNLPQY V SNELLEEA ...String:
MQSNKTFNLE KQNHTPRKHH QHHHQQHHQQ QQQQQQQPPP PIPANGQQAS SQNEGLTIDL KNFRKPGEKT FTQRSRLFVG NLPPDITEE EMRKLFEKYG KAGEVFIHKD KGFGFIRLET RTLAEIAKVE LDNMPLRGKQ LRVRFACHSA SLTVRNLPQY V SNELLEEA FSVFGQVERA VVIVDDRGRP SGKGIVEFSG KPAARKALDR CSEGSFLLTT FPRPVTVEPM DQLDDEEGLP EK LVIKNQQ FHKEREQPPR FAQPGSFEYE YAMRWKALIE MEKQQQDQVD RNIKEAREKL EMEMEAARHE HQVMLMRQDL MRR QEELRR MEELHNQEVQ KRKQLELRQE EERRRREEEM RRQQEEMMRR QQEGFKGTFP DAREQEIRMG QMAMGGAMGI NNRG AMPPA PVPTGTPAPP GPATMMPDGT LGLTPPTTER FGQAATMEGI GAIGGTPPAF NRPAPGADFA PNKRRRY

UniProtKB: Non-POU domain-containing octamer-binding protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
5.0 mMC10H16N2O8EDTA
0.03 %C24H46O11DDM
10.0 mMMgCl2magnesium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.04 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 5 sec, blot force +20.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 17059 / Average exposure time: 6.2 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4144650 / Details: blob picker
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: initial helical refinement
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2974535
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

6wmz

chain_id: A, residue_range: 367-589, source_name: PDB, initial_model_type: experimental modelSFPQ

6wmz

chain_id: B, residue_range: 148-307, source_name: PDB, initial_model_type: experimental modelNONO
Detailsfirst rigid fitting with Chimera, then further refinemnt with Coot, C-terminal some de-novo residues
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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