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- EMDB-53223: The structure of the DNA-binding domain of Nuclear Factor 1 X bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-53223
TitleThe structure of the DNA-binding domain of Nuclear Factor 1 X bound to NFI consensus DNA sequence
Map data
Sample
  • Complex: Transcription factor NFI-X/DNA superhelical complex
    • Protein or peptide: Nuclear factor 1 X-type
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
  • Ligand: ZINC ION
KeywordsTranscription factor / DNA-binding domain / MH1-like domain / CCCH motif / Zinc ion binding site / TRANSCRIPTION
Function / homology
Function and homology information


regeneration / glial cell fate specification / skeletal muscle satellite cell differentiation / epithelium development / osteoclast proliferation / atrioventricular canal morphogenesis / neuroblast migration / glial cell development / cerebellar granule cell differentiation / lateral ventricle development ...regeneration / glial cell fate specification / skeletal muscle satellite cell differentiation / epithelium development / osteoclast proliferation / atrioventricular canal morphogenesis / neuroblast migration / glial cell development / cerebellar granule cell differentiation / lateral ventricle development / cell proliferation in forebrain / neuron fate specification / neuroblast differentiation / ear development / collateral sprouting / cerebellar Purkinje cell layer development / cerebellar cortex morphogenesis / endochondral ossification / olfactory bulb development / tissue homeostasis / cellular response to BMP stimulus / forebrain radial glial cell differentiation / skeletal muscle tissue regeneration / exit from mitosis / camera-type eye development / astrocyte differentiation / brain morphogenesis / gliogenesis / neural precursor cell proliferation / stem cell population maintenance / generation of neurons / spinal cord development / bone mineralization / forebrain development / oligodendrocyte differentiation / macrophage differentiation / social behavior / neuroblast proliferation / phagocytosis / glial cell proliferation / cell maturation / skeletal muscle tissue development / Rho protein signal transduction / neurogenesis / homeostasis of number of cells within a tissue / osteoclast differentiation / cerebellum development / skeletal system development / learning / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / cerebral cortex development / response to wounding / multicellular organism growth / memory / cell morphogenesis / neuron differentiation / retina development in camera-type eye / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / chromatin binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
CTF transcription factor/nuclear factor 1 / CTF transcription factor/nuclear factor 1, N-terminal / CTF transcription factor/nuclear factor 1, conserved site / CTF/NF-I family transcription modulation region / Nuclear factor I protein pre-N-terminus / CTF/NF-I DNA-binding domain signature. / CTF transcription factor/nuclear factor 1, DNA-binding domain / CTF/NF-I DNA-binding domain profile. / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins
Similarity search - Domain/homology
Nuclear factor 1 X-type
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsTiberi M / Nardini M / Chaves-Sanjuan A / Gourlay LJ / Bonnet DMV
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural determinants of dimerization, activation and sequence-specific DNA binding by the transcription factor NFI-X: a prototype for the NFI family
Authors: Tiberi M / Nardini M / Chaves-Sanjuan A / Gourlay LJ / Bonnet DMV
History
DepositionMar 20, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53223.png

Downloads & links

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Map

FileDownload / File: emd_53223.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.8
Minimum - Maximum-1.8689255 - 3.4112422
Average (Standard dev.)0.0039982474 (±0.09866348)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 355.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53223_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_53223_additional_1.map
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Half map: #2

Fileemd_53223_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_53223_half_map_2.map
Projections & Slices
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Sample components

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Entire : Transcription factor NFI-X/DNA superhelical complex

EntireName: Transcription factor NFI-X/DNA superhelical complex
Components
  • Complex: Transcription factor NFI-X/DNA superhelical complex
    • Protein or peptide: Nuclear factor 1 X-type
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Transcription factor NFI-X/DNA superhelical complex

SupramoleculeName: Transcription factor NFI-X/DNA superhelical complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 62.5 KDa

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Macromolecule #1: Nuclear factor 1 X-type

MacromoleculeName: Nuclear factor 1 X-type / type: protein_or_peptide / ID: 1 / Details: The first histidine belongs to the tag / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.329928 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HMPFIEALLP HVRAFSYTWF NLQARKRKYF KKHEKRMSKD EERAVKDELL GEKPEIKQKW ASRLLAKLRK DIRPEFREDF VLTITGKKP PCCVLSNPDQ KGKIRRIDCL RQADKVWRLD LVMVILFKGI PLESTDGERL YKSPQCSNPG LCVQPHHIGV T IKELDLYL AYFVHTPESG QSDS

UniProtKB: Nuclear factor 1 X-type

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Macromolecule #2: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 2 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.547148 KDa
SequenceString:
(DG)(DG)(DG)(DT)(DC)(DT)(DC)(DT)(DT)(DT) (DG)(DG)(DC)(DA)(DG)(DG)(DC)(DA)(DG)(DC) (DC)(DA)(DA)(DC)(DC)(DA)(DG)(DC)(DA) (DA)(DA)

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Macromolecule #3: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 3 / Number of copies: 4 / Classification: DNA
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 9.520106 KDa
SequenceString:
(DT)(DT)(DT)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG)(DG)(DC)(DT)(DG)(DC)(DC)(DT)(DG)(DC) (DC)(DA)(DA)(DA)(DG)(DA)(DG)(DA)(DC) (DC)(DC)

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
50.0 mMTris-HCltris(hydroxymethyl)aminomethane
1.0 mMDTTDithiothreitol
GridModel: Quantifoil R0.6/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1225 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 44.618 Å
Applied symmetry - Helical parameters - Δ&Phi: 142.672 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 164794
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 201833 / Software - Name: RELION
Startup modelType of model: NONE / Details: ab initio
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7qqd


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qky:
The structure of the DNA-binding domain of Nuclear Factor 1 X bound to NFI consensus DNA sequence

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