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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 / collateral sprouting / ear development / cerebellar cortex morphogenesis / olfactory bulb development / endochondral ossification / cerebellar Purkinje cell layer 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 / generation of neurons / stem cell population maintenance / spinal cord development / bone mineralization / forebrain development / oligodendrocyte differentiation / macrophage differentiation / neuroblast proliferation / social behavior / phagocytosis / glial cell proliferation / skeletal muscle tissue development / cell maturation / Rho protein signal transduction / neurogenesis / homeostasis of number of cells within a tissue / osteoclast differentiation / cerebellum development / skeletal system development / learning / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / cerebral cortex development / brain development / response to wounding / memory / multicellular organism growth / 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: Nat Commun / Year: 2025
Title: Structural basis of Nuclear Factor 1-X DNA recognition provides prototypic insight into the NFI family.
Authors: Michele Tiberi / Michela Lapi / Louise Jane Gourlay / Antonio Chaves-Sanjuan / Maurizio Polentarutti / Nicola Demitri / Miriam Cavinato / Diane Marie Valérie Bonnet / Valentina Taglietti / ...Authors: Michele Tiberi / Michela Lapi / Louise Jane Gourlay / Antonio Chaves-Sanjuan / Maurizio Polentarutti / Nicola Demitri / Miriam Cavinato / Diane Marie Valérie Bonnet / Valentina Taglietti / Anna Righetti / Rachele Sala / Silvia Cauteruccio / Amit Kumawat / Rosaria Russo / Alberto Giuseppe Barbiroli / Nerina Gnesutta / Carlo Camilloni / Martino Bolognesi / Graziella Messina / Marco Nardini /
Abstract: Nuclear Factor I (NFI) proteins are involved in adenovirus DNA replication and regulate gene transcription, stem cell proliferation, and differentiation. They play key roles in development, cancer, ...Nuclear Factor I (NFI) proteins are involved in adenovirus DNA replication and regulate gene transcription, stem cell proliferation, and differentiation. They play key roles in development, cancer, and congenital disorders. Within the NFI family, NFI-X is critical for neural stem cell biology, hematopoiesis, muscle development, muscular dystrophies, and oncogenesis. Here, we present the structural characterization of the NFI transcription factor NFI-X, both alone and bound to its consensus palindromic DNA site. Our analyses reveal a MH1-like fold within NFI-X DNA-binding domain (DBD) and identify crucial structural determinants for activity, such as a Zn²⁺ binding site, dimeric assembly, and DNA-binding specificity. Given the ~85% sequence identity within the NFI DBDs, our structural data are prototypic for the entire family, a NFI Rosetta Stone that allows decoding a wealth of biochemical and functional data and provides a precise target for drug design in a wider disease context.
History
DepositionMar 20, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 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
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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

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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
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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
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Half map: #1

Fileemd_53223_half_map_2.map
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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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