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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 replication / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II ...RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA replication / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / 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: To Be Published
Title: Nuclear factor one X - NFIX in P41212
Authors: Lapi, M. / Chaves-Sanjuan, A. / Gourlay, L.J. / Tiberi, M. / Polentarutti, M. / Demitri, N. / Bais, G. / Nardini, M.
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

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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 / HEPES


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


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

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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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