[English] 日本語
Yorodumi
- PDB-4ep7: Functional implications from the Cid1 poly(U) polymerase crystal ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ep7
TitleFunctional implications from the Cid1 poly(U) polymerase crystal structure
ComponentsPoly(A) RNA polymerase protein cid1
KeywordsTRANSFERASE / poly(U) polymerase / UTP binding
Function / homology
Function and homology information


polyuridylation-dependent decapping of nuclear-transcribed mRNA / UTP binding / RNA uridylyltransferase / RNA 3' uridylation / RNA 3'-end processing / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / polynucleotide adenylyltransferase activity / nucleotidyltransferase activity / magnesium ion binding ...polyuridylation-dependent decapping of nuclear-transcribed mRNA / UTP binding / RNA uridylyltransferase / RNA 3' uridylation / RNA 3'-end processing / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / polynucleotide adenylyltransferase activity / nucleotidyltransferase activity / magnesium ion binding / RNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Poly(a)-polymerase, middle domain - #10 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / Cid1 family poly A polymerase / PAP/25A-associated / Nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily ...Poly(a)-polymerase, middle domain - #10 / TUTase nucleotidyltransferase domain / TUTase nucleotidyltransferase domain / Cid1 family poly A polymerase / PAP/25A-associated / Nucleotidyltransferase domain / Poly(a)-polymerase, middle domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2805 Å
AuthorsMunoz-Tello, P. / Gabus, C. / Thore, S.
CitationJournal: Structure / Year: 2012
Title: Functional implications from the cid1 poly(u) polymerase crystal structure.
Authors: Munoz-Tello, P. / Gabus, C. / Thore, S.
History
DepositionApr 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(A) RNA polymerase protein cid1
B: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,08211
Polymers77,9432
Non-polymers1,1389
Water4,396244
1
A: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5536
Polymers38,9721
Non-polymers5815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Poly(A) RNA polymerase protein cid1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5295
Polymers38,9721
Non-polymers5574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.490, 76.860, 81.860
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Poly(A) RNA polymerase protein cid1 / Caffeine-induced death protein 1


Mass: 38971.660 Da / Num. of mol.: 2 / Fragment: UNP Residues 40-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: cid1, SPAC19D5.03 / Production host: Escherichia coli (E. coli)
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 0.1M Imidatole/MES pH 6.1, 20% Glycerol, 10% PEG 4000, 42mM NaI, 42mM NaBr, 42mM NaF., VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9811 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2011
RadiationMonochromator: Channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9811 Å / Relative weight: 1
ReflectionResolution: 2.27→45.193 Å / Num. obs: 29999 / % possible obs: 97.4 % / Observed criterion σ(F): 2.64 / Observed criterion σ(I): 2.64 / Redundancy: 2.79 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.27-2.32.64711159.3
2.3-2.43.933501199.2
2.4-2.54.642942199.2
2.5-37.549607199.3
3-415.887653199.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_353)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2805→45.193 Å / SU ML: 0.34 / σ(F): 1.99 / Phase error: 24.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 1500 5 %RANDOM
Rwork0.1877 ---
obs0.1907 29996 98.74 %-
all-29996 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.058 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.926 Å2-0 Å22.7324 Å2
2---8.3656 Å20 Å2
3---2.4396 Å2
Refinement stepCycle: LAST / Resolution: 2.2805→45.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5146 0 65 244 5455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115459
X-RAY DIFFRACTIONf_angle_d1.1127188
X-RAY DIFFRACTIONf_dihedral_angle_d17.8322049
X-RAY DIFFRACTIONf_chiral_restr0.071778
X-RAY DIFFRACTIONf_plane_restr0.004898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2805-2.35410.28641330.2032540X-RAY DIFFRACTION97
2.3541-2.43830.2881370.19312587X-RAY DIFFRACTION99
2.4383-2.53590.25421360.192589X-RAY DIFFRACTION100
2.5359-2.65130.25161360.18342588X-RAY DIFFRACTION99
2.6513-2.79110.25911360.18252589X-RAY DIFFRACTION99
2.7911-2.96590.29511370.18912604X-RAY DIFFRACTION99
2.9659-3.19480.24011370.18222599X-RAY DIFFRACTION99
3.1948-3.51620.26651360.17412592X-RAY DIFFRACTION99
3.5162-4.02480.19361380.16682605X-RAY DIFFRACTION99
4.0248-5.06970.20691360.16092590X-RAY DIFFRACTION98
5.0697-45.20210.24681380.20972613X-RAY DIFFRACTION97

+
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