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- PDB-7njc: Crystal structure of the Toxoplasma CPSF4 YTH-domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 7njc
TitleCrystal structure of the Toxoplasma CPSF4 YTH-domain in complex with a 7 mer m6A-modified RNA
Components
  • RNA (5'-R(*(6MZ)P*CP*A)-3')
  • Zinc finger (CCCH type) motif-containing protein
KeywordsRNA BINDING PROTEIN / YTH / Cleavage and Polyadenylation / RNA / m6A / RNA recognition protein
Function / homology
Function and homology information


N6-methyladenosine-containing RNA reader activity / regulation of mRNA splicing, via spliceosome / mRNA splicing, via spliceosome / mRNA binding / zinc ion binding / nucleoplasm
Similarity search - Function
YTH domain containing protein / YTH domain / YT521-B-like domain / YTH domain profile. / Zinc finger, CCCH-type superfamily / zinc finger / Zinc finger, CCCH-type / Zinc finger C3H1-type profile.
Similarity search - Domain/homology
N-methyladenosine / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / RNA / Zinc finger (CCCH type) motif-containing protein
Similarity search - Component
Biological speciesToxoplasma gondii (eukaryote)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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 16, 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
B: RNA (5'-R(*(6MZ)P*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1134
Polymers20,6672
Non-polymers4452
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-9 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.442, 35.153, 38.350
Angle α, β, γ (deg.)114.679, 100.702, 97.653
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 / Variant (production host): BL21-RIL / References: UniProt: S8F6K2
#2: RNA chain RNA (5'-R(*(6MZ)P*CP*A)-3')


Mass: 2219.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Modified N6-Adenosine / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#4: Chemical ChemComp-6MD / N-methyladenosine


Mass: 281.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 1.84 Å3/Da / Density % sol: 33.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH: 4.6 in 40% PEG 200

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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 EIGER2 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: 1.38→31.04 Å / Num. obs: 19180 / % possible obs: 62.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 18.45 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.3
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 288 / CC1/2: 0.989 / % possible all: 6.5

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Processing

Software
NameVersionClassification
XDSdata reduction
STARANISOdata processing
Aimlessdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4r3i

4r3i


Resolution: 1.38→31.04 Å / SU ML: 0.0986 / Cross valid method: FREE R-VALUE / σ(F): 2.13 / Phase error: 21.2755
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1685 1918 10 %
Rwork0.143 17262 -
obs0.1456 19180 62.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.72 Å2
Refinement stepCycle: LAST / Resolution: 1.38→31.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 42 31 61 1312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561302
X-RAY DIFFRACTIONf_angle_d0.91541769
X-RAY DIFFRACTIONf_chiral_restr0.44190
X-RAY DIFFRACTIONf_plane_restr0.0047217
X-RAY DIFFRACTIONf_dihedral_angle_d12.6246486
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.410.189880.162276X-RAY DIFFRACTION3.82
1.41-1.450.1883190.162171X-RAY DIFFRACTION8.97
1.45-1.490.1448370.1038333X-RAY DIFFRACTION16.93
1.49-1.540.1617540.1127482X-RAY DIFFRACTION24.31
1.54-1.590.1385750.1029675X-RAY DIFFRACTION34.53
1.59-1.660.16961020.1135919X-RAY DIFFRACTION46.81
1.66-1.730.16091480.11051337X-RAY DIFFRACTION69.04
1.73-1.820.16712080.11611868X-RAY DIFFRACTION94.71
1.83-1.940.14942080.11671875X-RAY DIFFRACTION96.26
1.94-2.090.15562110.12541893X-RAY DIFFRACTION96.51
2.09-2.30.16072120.13541913X-RAY DIFFRACTION97.21
2.3-2.630.1732110.15751901X-RAY DIFFRACTION97.33
2.63-3.310.17962120.16281898X-RAY DIFFRACTION96.92
3.32-31.040.17642130.15881921X-RAY DIFFRACTION97.62

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