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- PDB-9qky: The structure of the DNA-binding domain of Nuclear Factor 1 X bou... -

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Basic information

Entry
Database: PDB / ID: 9qky
TitleThe structure of the DNA-binding domain of Nuclear Factor 1 X bound to NFI consensus DNA sequence
Components
  • (DNA (31-MER)) x 2
  • Nuclear factor 1 X-type
KeywordsTRANSCRIPTION / Transcription factor / DNA-binding domain / MH1-like domain / CCCH motif / Zinc ion binding site
Function / homology
Function and homology information


neuroblast migration / regeneration / glial cell fate specification / epithelium development / skeletal muscle satellite cell differentiation / osteoclast proliferation / glial cell development / atrioventricular canal morphogenesis / ear development / cerebellar granule cell differentiation ...neuroblast migration / regeneration / glial cell fate specification / epithelium development / skeletal muscle satellite cell differentiation / osteoclast proliferation / glial cell development / atrioventricular canal morphogenesis / ear development / cerebellar granule cell differentiation / neuron fate specification / collateral sprouting / lateral ventricle development / cell proliferation in forebrain / forebrain radial glial cell differentiation / endochondral ossification / neuroblast differentiation / exit from mitosis / tissue homeostasis / olfactory bulb development / cerebellar cortex morphogenesis / cellular response to BMP stimulus / cerebellar Purkinje cell layer development / brain morphogenesis / camera-type eye development / skeletal muscle tissue regeneration / astrocyte differentiation / oligodendrocyte differentiation / neural precursor cell proliferation / gliogenesis / forebrain development / stem cell population maintenance / neuroblast proliferation / generation of neurons / bone mineralization / spinal cord development / retina development in camera-type eye / macrophage differentiation / social behavior / skeletal muscle tissue development / homeostasis of number of cells within a tissue / glial cell proliferation / cell maturation / osteoclast differentiation / phagocytosis / multicellular organism growth / neurogenesis / Rho protein signal transduction / skeletal system development / cerebellum development / learning / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / brain development / cerebral cortex development / cell morphogenesis / response to wounding / memory / gene expression / neuron differentiation / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA-binding transcription activator activity, RNA polymerase II-specific / negative regulation of neuron apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / inflammatory response / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / 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
DNA / DNA (> 10) / Nuclear factor 1 X-type
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsTiberi, M. / Nardini, M. / Chaves-Sanjuan, A. / Gourlay, L.J. / Bonnet, D.M.V.
Funding support1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor 1 X-type
B: Nuclear factor 1 X-type
C: DNA (31-MER)
D: DNA (31-MER)
E: Nuclear factor 1 X-type
F: Nuclear factor 1 X-type
G: DNA (31-MER)
H: DNA (31-MER)
I: Nuclear factor 1 X-type
J: Nuclear factor 1 X-type
K: DNA (31-MER)
L: DNA (31-MER)
M: Nuclear factor 1 X-type
N: Nuclear factor 1 X-type
O: DNA (31-MER)
P: DNA (31-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,43224
Polymers246,90816
Non-polymers5238
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Nuclear factor 1 X-type / NF1-X / Nuclear factor 1/X / CCAAT-box-binding transcription factor / CTF / Nuclear factor I/X / NF- ...NF1-X / Nuclear factor 1/X / CCAAT-box-binding transcription factor / CTF / Nuclear factor I/X / NF-I/X / NFI-X / TGGCA-binding protein


Mass: 21329.928 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: The first histidine belongs to the tag / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfix / Variant: isoform 2 / Plasmid: His-SUMO-pET21b / Details (production host): modified pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle(DE3) / References: UniProt: P70257
#2: DNA chain
DNA (31-MER)


Mass: 9547.148 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: DNA chain
DNA (31-MER)


Mass: 9520.106 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Transcription factor NFI-X/DNA superhelical complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.0625 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: SHuffle
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
250 mMtris(hydroxymethyl)aminomethaneTris-HCl1
31 mMDithiothreitolDTT1
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1225

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
14PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 142.672 ° / Axial rise/subunit: 44.618 Å / Axial symmetry: D1
Particle selectionNum. of particles selected: 201833
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 164794 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7QQD

7qqd


Pdb chain-ID: A / Accession code: 7QQD / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.86 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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