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- PDB-7ng2: Crystal structure of Toxoplasma CPSF4-YTH domain in apo form -

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Basic information

Entry
Database: PDB / ID: 7ng2
TitleCrystal structure of Toxoplasma CPSF4-YTH domain in apo form
ComponentsZinc finger (CCCH type) motif-containing protein
KeywordsRNA BINDING PROTEIN / YTH / Cleavage and Polyadenylation / RNA / m6A
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / regulation of alternative mRNA splicing, via spliceosome / mRNA splicing, via spliceosome / mRNA binding / nucleoplasm / metal ion binding
Similarity search - Function
YTH domain containing protein / Zinc finger, CCCH-type superfamily / YTH domain / YT521-B-like domain / YTH domain profile. / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Zinc finger (CCCH type) motif-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.23 Å
AuthorsSwale, C. / Bowler, M.W.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Laboratories of Excellence (LabEx)ANR-11-LABX-0024 France
European Research Council (ERC)614880European Union
CitationJournal: Elife / Year: 2021
Title: A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma .
Authors: Farhat, D.C. / Bowler, M.W. / Communie, G. / Pontier, D. / Belmudes, L. / Mas, C. / Corrao, C. / Coute, Y. / Bougdour, A. / Lagrange, T. / Hakimi, M.A. / Swale, C.
History
DepositionFeb 8, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger (CCCH type) motif-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5082
Polymers18,4481
Non-polymers601
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint5 kcal/mol
Surface area8270 Å2
Unit cell
Length a, b, c (Å)40.180, 40.180, 202.600
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

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Components

#1: Protein Zinc finger (CCCH type) motif-containing protein / CPSF4


Mass: 18447.994 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Toxoplasma gondii (strain ATCC 50611 / Me49) (eukaryote)
Strain: ATCC 50611 / Me49 / Gene: TGME49_201200 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: S8F6K2
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20 % PEG 4000, 20% isopropanol and 0.1M tri-sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.23→34.53 Å / Num. obs: 49444 / % possible obs: 99.32 % / Redundancy: 11 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 1 / Net I/σ(I): 20.3
Reflection shellResolution: 1.23→1.274 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4552 / CC1/2: 0.427 / % possible all: 93.7

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Processing

Software
NameVersionClassification
DIALSdata scaling
PHENIXdata reduction
PHASERphasing
PHENIXmodel building
PHENIX1.17.1refinement
PDB-REDOmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3i

4r3i


Resolution: 1.23→34.53 Å / SU ML: 0.1571 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.8726
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2038 2500 5.06 %
Rwork0.1767 46941 -
obs0.1781 49441 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.56 Å2
Refinement stepCycle: LAST / Resolution: 1.23→34.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 4 150 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461337
X-RAY DIFFRACTIONf_angle_d0.77091822
X-RAY DIFFRACTIONf_chiral_restr0.0789193
X-RAY DIFFRACTIONf_plane_restr0.0049240
X-RAY DIFFRACTIONf_dihedral_angle_d14.5699496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.280.3161510.31262451X-RAY DIFFRACTION97.27
1.28-1.310.28681510.26822551X-RAY DIFFRACTION99.59
1.31-1.340.24961390.22852576X-RAY DIFFRACTION99.96
1.34-1.370.21881050.19652585X-RAY DIFFRACTION100
1.37-1.410.23191310.18562581X-RAY DIFFRACTION100
1.41-1.450.22061470.18422595X-RAY DIFFRACTION99.93
1.45-1.50.23881410.18452603X-RAY DIFFRACTION100
1.5-1.550.22411380.1792589X-RAY DIFFRACTION100
1.55-1.610.19691550.15942570X-RAY DIFFRACTION100
1.61-1.690.17631350.14342600X-RAY DIFFRACTION100
1.69-1.770.17721380.13742606X-RAY DIFFRACTION100
1.77-1.890.17091380.16272617X-RAY DIFFRACTION100
1.89-2.030.19681300.16662668X-RAY DIFFRACTION99.96
2.03-2.230.16781300.15712669X-RAY DIFFRACTION99.89
2.23-2.560.19351580.1682651X-RAY DIFFRACTION99.93
2.56-3.220.22751460.18222722X-RAY DIFFRACTION99.86

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