[English] 日本語
Yorodumi
- PDB-9qky: The structure of the DNA-binding domain of Nuclear Factor 1 X bou... -

+
Open data


ID or keywords:

Loading...

-
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 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 / 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 / brain development / cerebral cortex 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more