[English] 日本語
Yorodumi
- PDB-7njc: Crystal structure of the Toxoplasma CPSF4 YTH-domain in complex w... -

+
Open data


ID or keywords:

Loading...

-
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


RNA binding / 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-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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / N6-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 / Water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more