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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


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 / social behavior / neuroblast proliferation / 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
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: 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, L.J. / Bonnet, D.M.V.
History
DepositionMar 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 17, 2025Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Sep 17, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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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