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- PDB-7nh2: Crystal structure of Toxoplasma CPSF4-YTH domain bound to m6A -

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Basic information

Entry
Database: PDB / ID: 7nh2
TitleCrystal structure of Toxoplasma CPSF4-YTH domain bound to m6A
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
~{N},9-dimethylpurin-6-amine / Zinc finger (CCCH type) motif-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 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 9, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,8053
Polymers18,4481
Non-polymers3572
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Checked using size exclusion chromatography combined with multi-angle laser light scattering.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint7 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.474, 35.221, 38.177
Angle α, β, γ (deg.)114.510, 100.436, 97.766
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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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-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Chemical ChemComp-OYK / ~{N},9-dimethylpurin-6-amine


Mass: 163.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H9N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 50% PEG 400, 0.1M Sodium acetate pH 4.5 and 0.2M LiSO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.349→30.76 Å / Num. obs: 30036 / % possible obs: 92.64 % / Redundancy: 1.6 % / Biso Wilson estimate: 9.18 Å2 / CC1/2: 0.956 / Net I/σ(I): 6.6
Reflection shellResolution: 1.349→1.397 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2887 / CC1/2: 0.496 / % possible all: 88.38

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Processing

Software
NameVersionClassification
DIALSdata processing
DIALSdata scaling
PHASERphasing
PHENIXmodel building
PHENIX1.17.1_3660refinement
PDB-REDOmodel building
xia2data reduction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3i

4r3i


Resolution: 1.35→30.76 Å / SU ML: 0.1393 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 20.9977
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1967 1532 5.11 %
Rwork0.1825 28475 -
obs0.1832 30007 92.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 23 148 1356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531298
X-RAY DIFFRACTIONf_angle_d0.82181762
X-RAY DIFFRACTIONf_chiral_restr0.0774185
X-RAY DIFFRACTIONf_plane_restr0.0043227
X-RAY DIFFRACTIONf_dihedral_angle_d15.8072485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.390.26091390.24162456X-RAY DIFFRACTION88.12
1.39-1.440.22791220.22962531X-RAY DIFFRACTION89.99
1.44-1.50.22291230.21742560X-RAY DIFFRACTION90.64
1.5-1.570.23771350.21072504X-RAY DIFFRACTION90.62
1.57-1.650.23161310.19472607X-RAY DIFFRACTION92.41
1.65-1.750.19761510.17762630X-RAY DIFFRACTION94.27
1.75-1.890.19911310.17782631X-RAY DIFFRACTION93.5
1.89-2.080.17451490.16382584X-RAY DIFFRACTION93.31
2.08-2.380.18491480.16182631X-RAY DIFFRACTION94.3
2.38-30.18291520.18132618X-RAY DIFFRACTION94.38
3-30.760.18931510.17482723X-RAY DIFFRACTION97.59

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