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- PDB-9eve: Crystal structure of the ARM domain of human ZNFX1 -

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Basic information

Entry
Database: PDB / ID: 9eve
TitleCrystal structure of the ARM domain of human ZNFX1
ComponentsNFX1-type zinc finger-containing protein 1
KeywordsRNA BINDING PROTEIN / Helicase / E3 ligase / armadillo domain
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / activation of innate immune response / helicase activity / cytoplasmic stress granule / defense response to virus / mitochondrial outer membrane / defense response to bacterium / innate immune response ...nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / activation of innate immune response / helicase activity / cytoplasmic stress granule / defense response to virus / mitochondrial outer membrane / defense response to bacterium / innate immune response / RNA binding / zinc ion binding
Similarity search - Function
Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal ...Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NFX1-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.67 Å
AuthorsGrabarczyk, D.B. / Deszcz, L. / Clausen, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: To Be Published
Title: Antiviral mechanism of the non-canonical E3 ligase ZNFX1
Authors: Grabarczyk, D.B. / Clausen, T.
History
DepositionMar 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NFX1-type zinc finger-containing protein 1
B: NFX1-type zinc finger-containing protein 1


Theoretical massNumber of molelcules
Total (without water)44,9262
Polymers44,9262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.850, 51.570, 86.650
Angle α, β, γ (deg.)90.000, 101.746, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 17 - 189 / Label seq-ID: 17 - 189

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.909738830297, -0.0293364556705, 0.414143251808), (-0.0317716052761, -0.999494646069, -0.00100875084877), (0.413963556062, -0.012240296107, -0.910211156493)Vector: -9. ...NCS oper: (Code: given
Matrix: (0.909738830297, -0.0293364556705, 0.414143251808), (-0.0317716052761, -0.999494646069, -0.00100875084877), (0.413963556062, -0.012240296107, -0.910211156493)
Vector: -9.15069227013, -0.287125859414, 42.2222612432)

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Components

#1: Protein NFX1-type zinc finger-containing protein 1


Mass: 22463.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNFX1, KIAA1404 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2E3
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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, NaCl, citrate pH 4.2, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.67→51.57 Å / Num. obs: 4452 / % possible obs: 97.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 66.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 3.67→4.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 12 / Num. unique obs: 961 / CC1/2: 0.995 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.67→44.3 Å / SU ML: 0.516 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 462 10.45 %
Rwork0.1978 3961 -
obs0.2019 4423 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.37 Å2
Refinement stepCycle: LAST / Resolution: 3.67→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 0 2698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212732
X-RAY DIFFRACTIONf_angle_d0.48443686
X-RAY DIFFRACTIONf_chiral_restr0.0357454
X-RAY DIFFRACTIONf_plane_restr0.0043460
X-RAY DIFFRACTIONf_dihedral_angle_d13.29861058
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.398054491818 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.67-4.20.27041360.20381240X-RAY DIFFRACTION92.1
4.2-5.290.23641590.18521348X-RAY DIFFRACTION99.41
5.29-44.30.21581670.20471373X-RAY DIFFRACTION99.1

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