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- EMDB-51413: NONO/SFPQ filament, overall map -

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Basic information

Entry
Database: EMDB / ID: EMD-51413
TitleNONO/SFPQ filament, overall map
Map dataoverall map after non-uniform refinement, sharpened with Phenix autosharpen B = 50
Sample
  • Complex: filament of NONO and SFPQ
    • 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: 3.9 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_51413.png

Downloads & links

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Map

FileDownload / File: emd_51413.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationoverall map after non-uniform 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: 5.0
Minimum - Maximum-11.622741 - 37.676990000000004
Average (Standard dev.)0.000000000000153 (±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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Half map: half map A

Fileemd_51413_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_51413_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 : filament of NONO and SFPQ

EntireName: filament of NONO and SFPQ
Components
  • Complex: filament of NONO and SFPQ
    • 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: filament of NONO and SFPQ

SupramoleculeName: filament of NONO and SFPQ / 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 PPPQQPPPQQ PPPHQQPPPH QPPHQQPPPP PQDSSKPVVP QGPGSAPGVS PAPPPAGSAP PANPPTTGAP PGPGPTPTPP PAVTSATPGP PPPSTPSSGV ...String:
MSRDRFRSRG GGGGGFHRRG GGGGRGGLHD FRSPPPGMGL NQNRGPMGPG PGGPKPPIPP PPPHQQQPQQ PPPQQPPPQQ PPPHQQPPPH QPPHQQPPPP PQDSSKPVVP QGPGSAPGVS PAPPPAGSAP PANPPTTGAP PGPGPTPTPP PAVTSATPGP PPPSTPSSGV STTPPQSGGP PPPPAGGAGP GPKQGPGPGP GGPKGGKMPG GPKPGGGPGM GAPGGHPKPP HRGGGEPRGG RQHHPPYHQQ HHQGPPPGGP AARTEEKISD SEGFKANLSL LRRPGEKTYT QRCRLFVGNL PADITEDEFK RLFAKYGEPG EVFINKGKGF GFIKLESRAL AEIAKAELDD TPMRGRQLRV RFATHAAALS VRNLSPYVSN ELLEEAFSQF GPIERAVVIV DDRGRSTGKG IVEFASKPAA RKAFERCSEG VFLLTTTPRP VIVEPLEQLD DEDGLPEKLA QKNPMYQKER ETPPRFAQHG TFEYEYSQRW KSLDEMEKQQ REQVEKNMKD AKDKLESEME DAYHEHQANL LRQDLMRRQE ELRRMEELHS QEMQKRKEMQ LRQEEERRRR EEEMMIRQRE MEEQMRRQRE ESYSRMGYMD PRERDMRMGG GGTMNMGDPY GSGGQKFPPL GGGGGIGYEA NPGVPPATMS GSMMGSDMVR MIDVG

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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 mMMgCl2magnisium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / 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 / Details: 5 sec blotting, +20 blot force.

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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: 3.9 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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