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- PDB-7qqe: Nuclear factor one X - NFIX in P41212 -

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Basic information

Entry
Database: PDB / ID: 7qqe
TitleNuclear factor one X - NFIX in P41212
ComponentsNuclear factor 1 X-type
KeywordsDNA BINDING PROTEIN / Transcription Factor / NFI / NFIX / NF-1
Function / homology
Function and homology information


RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin ...RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLapi, M. / Chaves-Sanjuan, A. / Gourlay, L.J. / Tiberi, M. / Polentarutti, M. / Demitri, N. / Bais, G. / Nardini, M.
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
DepositionJan 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Dec 24, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0125
Polymers19,5771
Non-polymers4354
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-43 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.009, 65.009, 127.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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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: 19577.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first GSHM belongs to a Thrombin cleavage stie / Source: (gene. exp.) Homo sapiens (human) / Gene: NFIX / Production host: Escherichia coli (E. coli) / References: UniProt: Q14938
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaSCN, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1.28199 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28199 Å / Relative weight: 1
ReflectionResolution: 3.5→45.97 Å / Num. obs: 3802 / % possible obs: 100 % / Redundancy: 25.1 % / Biso Wilson estimate: 113.17 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.116 / Net I/σ(I): 7.6
Reflection shellResolution: 3.5→3.85 Å / Redundancy: 26.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 366 / CC1/2: 0.603 / Rpim(I) all: 0.919 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.9refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QQD

7qqd


Resolution: 3.5→45.59 Å / SU ML: -0 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.1005
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2589 187 4.92 %
Rwork0.223 3615 -
obs0.2247 3802 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 121.93 Å2
Refinement stepCycle: LAST / Resolution: 3.5→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1344 0 18 6 1368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071390
X-RAY DIFFRACTIONf_angle_d1.03081866
X-RAY DIFFRACTIONf_chiral_restr0.061197
X-RAY DIFFRACTIONf_plane_restr0.0066234
X-RAY DIFFRACTIONf_dihedral_angle_d22.5652560
LS refinement shellResolution: 3.5→45.59 Å
RfactorNum. reflection% reflection
Rfree0.2589 187 -
Rwork0.223 3615 -
obs--99.89 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3449102792380.132000872544-0.2305813530570.468692283324-0.1073723329960.145084491283-0.046583631314-0.2309730083431.72507591970.310995845760.136290847751-0.4243425210021.60444016096-0.112712475654-2.25181187072E-61.166875408590.1964943297780.04691413132461.01287664472-0.18540778361.2938974734921.435666859414.070878928416.4833626628
21.34970764121.0993930628-1.203791805673.1344479732-1.121079134573.82453514470.02821036076150.2951950262980.0817046934912-0.228565323529-0.07202558777010.1733725086630.17342351760.507081691891-1.29368627181E-81.22382152924-0.00663841815209-0.07864874481451.049566605380.01362389740081.2335123347918.417682723.26445972767.83956843182
35.15472988570.4034561050361.019397189561.483883697022.223776779193.1009196792-0.3554344015470.481498010707-0.685494919676-0.5429912868720.243282209322-0.169390126481.111337958920.5807348056233.60198749102E-91.402338474390.107851294565-0.02985880267481.16306761016-0.08460632708021.1471608847526.6493452326.49230834236-0.44554281204
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 11 through 24 )11 - 241 - 14
22chain 'A' and (resid 25 through 105 )25 - 10515 - 95
33chain 'A' and (resid 106 through 173 )106 - 17396 - 163

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