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- PDB-9ci7: Structure of PNUTS:Tox4 complex -

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Basic information

Entry
Database: PDB / ID: 9ci7
TitleStructure of PNUTS:Tox4 complex
Components
  • Serine/threonine-protein phosphatase 1 regulatory subunit 10
  • TOX high mobility group box family member 4
KeywordsSIGNALING PROTEIN / PNUTS / PPP1R10 / Transcriptional elongation factor S-II homology N-terminal domain. Tox4 / zinc binding protein / complex
Function / homology
Function and homology information


negative regulation of mitotic DNA damage checkpoint / PTW/PP1 phosphatase complex / protein phosphatase 1 binding / negative regulation of cardiac muscle cell apoptotic process / protein phosphatase inhibitor activity / positive regulation of telomere maintenance / chromatin DNA binding / chromosome, telomeric region / nuclear body / regulation of transcription by RNA polymerase II ...negative regulation of mitotic DNA damage checkpoint / PTW/PP1 phosphatase complex / protein phosphatase 1 binding / negative regulation of cardiac muscle cell apoptotic process / protein phosphatase inhibitor activity / positive regulation of telomere maintenance / chromatin DNA binding / chromosome, telomeric region / nuclear body / regulation of transcription by RNA polymerase II / chromatin / DNA binding / RNA binding / zinc ion binding / nucleus
Similarity search - Function
: / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Zinc finger, CCCH-type superfamily / zinc finger / TFIIS/LEDGF domain superfamily ...: / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Zinc finger C-x8-C-x5-C-x3-H type (and similar) / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Zinc finger, CCCH-type superfamily / zinc finger / TFIIS/LEDGF domain superfamily / Zinc finger, CCCH-type / Zinc finger C3H1-type profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 1 regulatory subunit 10 / TOX high mobility group box family member 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsPage, R. / Peti, W. / Wang, X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)144379 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)144483 United States
CitationJournal: Cell Rep / Year: 2025
Title: PNUTS:PP1 recruitment to Tox4 regulates chromosomal dispersal in Drosophila germline development.
Authors: Duncalf, L. / Wang, X. / Aljabri, A.A. / Campbell, A.E. / Alharbi, R.Q. / Donaldson, I. / Hayes, A. / Peti, W. / Page, R. / Bennett, D.
History
DepositionJul 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 1 regulatory subunit 10
B: TOX high mobility group box family member 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5059
Polymers24,2092
Non-polymers2967
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-90 kcal/mol
Surface area10930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.630, 70.630, 97.165
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Serine/threonine-protein phosphatase 1 regulatory subunit 10 / MHC class I region proline-rich protein CAT53 / Phosphatase 1 nuclear targeting subunit / Protein PNUTS


Mass: 18029.049 Da / Num. of mol.: 1 / Mutation: C48S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ppp1r10, Cat53, Pnuts / Production host: Escherichia coli (E. coli) / References: UniProt: O55000
#2: Protein TOX high mobility group box family member 4 / Epidermal Langerhans cell protein LCP1


Mass: 6180.001 Da / Num. of mol.: 1 / Mutation: C601S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOX4, C14orf92, KIAA0737 / Production host: Escherichia coli (E. coli) / References: UniProt: O94842

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Non-polymers , 4 types, 135 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 100 mM MES pH 6.5, 1 M LiCl, 15% PEG6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.192 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.192 Å / Relative weight: 1
ReflectionResolution: 2.1→38.04 Å / Num. obs: 15943 / % possible obs: 98.8 % / Redundancy: 2.8 % / Biso Wilson estimate: 38.74 Å2 / CC1/2: 0.973 / Rmerge(I) obs: 0.067 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.498 / Num. unique obs: 1260 / CC1/2: 0.735

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Processing

Software
NameVersionClassification
RESOLVEmodel building
PHENIX1.19.1_4122refinement
XDSdata reduction
SOLVEphasing
Cootmodel building
Aimlessdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→35.32 Å / SU ML: 0.2166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8137
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2167 783 4.92 %
Rwork0.1882 15133 -
obs0.1896 15916 98.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→35.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1581 0 7 128 1716
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00121629
X-RAY DIFFRACTIONf_angle_d0.3362204
X-RAY DIFFRACTIONf_chiral_restr0.0326258
X-RAY DIFFRACTIONf_plane_restr0.0025276
X-RAY DIFFRACTIONf_dihedral_angle_d10.0886619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.28881400.24762459X-RAY DIFFRACTION97.12
2.23-2.40.22611210.20412539X-RAY DIFFRACTION99.25
2.4-2.640.27491420.24132517X-RAY DIFFRACTION99.55
2.64-3.030.27031400.22162512X-RAY DIFFRACTION98.66
3.03-3.810.22691070.19872569X-RAY DIFFRACTION99.78
3.81-35.320.15551330.14552537X-RAY DIFFRACTION98.13

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