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- EMDB-51417: NONO/SFPQ filament: local refinement single strand (strand 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-51417
TitleNONO/SFPQ filament: local refinement single strand (strand 1)
Map datalocal refinement of one strand (strand 1), sharpened with Phenix-autosharpen B = 50
Sample
  • Complex: NONO/SFPQ filament
    • Protein or peptide: splicing factor proline/glutamine rich (SFPQ)
    • Protein or peptide: Non-POU domain-containing octamer-binding protein (NONO)
Keywordsfilament / RNA binding / DNA binding / gene regulation / NUCLEAR PROTEIN
Biological speciesCricetulus griseus (Chinese hamster)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 23, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51417.png

Downloads & links

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Map

FileDownload / File: emd_51417.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationlocal refinement of one strand (strand 1), 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: 7.0
Minimum - Maximum-55.055954 - 79.934160000000006
Average (Standard dev.)0.000000000003637 (±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_51417_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_51417_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_51417_half_map_2.map
Annotationhalf map A
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 (SFPQ)
    • Protein or peptide: Non-POU domain-containing octamer-binding protein (NONO)

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Supramolecule #1: NONO/SFPQ filament

SupramoleculeName: NONO/SFPQ filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cricetulus griseus (Chinese hamster)

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Macromolecule #1: splicing factor proline/glutamine rich (SFPQ)

MacromoleculeName: splicing factor proline/glutamine rich (SFPQ) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
SequenceString: MSRDRFRSRG GGGGGFHRRG GGGGRGGLHD FRSPPPGMGL NQNRGPMGPG PGGPKPPIPP PPPHQQQPQQ PPPQQPPPQ QPPPHQQPPP HQPPHQQPPP PPQDSSKPVV PQGPGSAPGV SPAPPPAGSA PPANPPTTGA P PGPGPTPT PPPAVTSATP GPPPPSTPSS ...String:
MSRDRFRSRG GGGGGFHRRG GGGGRGGLHD FRSPPPGMGL NQNRGPMGPG PGGPKPPIPP PPPHQQQPQQ PPPQQPPPQ QPPPHQQPPP HQPPHQQPPP PPQDSSKPVV PQGPGSAPGV SPAPPPAGSA PPANPPTTGA P PGPGPTPT PPPAVTSATP GPPPPSTPSS GVSTTPPQSG GPPPPPAGGA GPGPKQGPGP GPGGPKGGKM PG GPKPGGG PGMGAPGGHP KPPHRGGGEP RGGRQHHPPY HQQHHQGPPP GGPAARTEEK ISDSEGFKAN LSL LRRPGE KTYTQRCRLF VGNLPADITE DEFKRLFAKY GEPGEVFINK GKGFGFIKLE SRALAEIAKA ELDD TPMRG RQLRVRFATH AAALSVRNLS PYVSNELLEE AFSQFGPIER AVVIVDDRGR STGKGIVEFA SKPAA RKAF ERCSEGVFLL TTTPRPVIVE PLEQLDDEDG LPEKLAQKNP MYQKERETPP RFAQHGTFEY EYSQRW KSL DEMEKQQREQ VEKNMKDAKD KLESEMEDAY HEHQANLLRQ DLMRRQEELR RMEELHSQEM QKRKEMQ LR QEEERRRREE EMMIRQREME EQMRRQREES YSRMGYMDPR ERDMRMGGGG TMNMGDPYGS GGQKFPPL G GGGGIGYEAN PGVPPATMSG SMMGSDMVRM IDVG

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Macromolecule #2: Non-POU domain-containing octamer-binding protein (NONO)

MacromoleculeName: Non-POU domain-containing octamer-binding protein (NONO)
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Cricetulus griseus (Chinese hamster)
SequenceString: MQSNKTFNLE KQNHTPRKHH QHHHQQHHQQ QQQQQQPPPP IPANGQQASS QNEGLTIDLK NFRKPGEKTF TQRSRLFVG NLPPDITEEE MRKLFEKYGK AGEVFIHKDK GFGFIRLETR TLAEIAKVEL DNMPLRGKQL R VRFACHSA SLTVRNLPQY VSNELLEEAF ...String:
MQSNKTFNLE KQNHTPRKHH QHHHQQHHQQ QQQQQQPPPP IPANGQQASS QNEGLTIDLK NFRKPGEKTF TQRSRLFVG NLPPDITEEE MRKLFEKYGK AGEVFIHKDK GFGFIRLETR TLAEIAKVEL DNMPLRGKQL R VRFACHSA SLTVRNLPQY VSNELLEEAF SVFGQVERAV VIVDDRGRPS GKGIVEFSGK PAARKALDRC SE GSFLLTT FPRPVTVEPM DQLDDEEGLP EKLVIKNQQF HKEREQPPRF AQPGSFEYEY AMRWKALIEM EKQ QQDQVD RNIKEAREKL EMEMEAARHE HQVMLMRQDL MRRQEELRRM EELHNQEVQK RKQLELRQEE ERRR REEEM RRQQEEMMRR QQEGFKGTFP DAREQEIRMG QMAMGGAMGI NNRGAMPPAP VPTGTPAPPG PATMM PDGT LGLTPPTTER FGQAATMEGI GAIGGTPPAF NRPAPGADFA PNKRRRY

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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 chlordie
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / 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

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Electron microscopy

MicroscopeFEI TITAN 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
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: initial helical refinement
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 2974535
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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