[English] 日本語
Yorodumi
- PDB-4ud5: Structural Plasticity of Cid1 Provides a Basis for its RNA Termin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ud5
TitleStructural Plasticity of Cid1 Provides a Basis for its RNA Terminal Uridylyl Transferase Activity
ComponentsPOLY(A) RNA POLYMERASE PROTEIN CID1
KeywordsTRANSFERASE / CAFFEINE / URIDYLYLTRANSFERASE ENZYME
Function / homology
Function and homology information


polyuridylation-dependent decapping of nuclear-transcribed mRNA / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / magnesium ion binding / RNA binding / ATP binding ...polyuridylation-dependent decapping of nuclear-transcribed mRNA / RNA 3' uridylation / RNA uridylyltransferase / RNA uridylyltransferase activity / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / UTP binding / magnesium ion binding / RNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Poly(a)-polymerase, middle domain - #10 / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich ...Poly(a)-polymerase, middle domain - #10 / PAP/25A-associated / Cid1 family poly A polymerase / Poly(A) RNA polymerase, mitochondrial-like, central palm domain / Poly(a)-polymerase, middle domain / Nucleotidyltransferase domain / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Terminal uridylyltransferase cid1
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsYates, L.A. / Durrant, B.P. / Fleurdepine, S. / Harlos, K. / Norbury, C.J. / Gilbert, R.J.C.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural Plasticity of Cid1 Provides a Basis for its Distributive RNA Terminal Uridylyl Transferase Activity.
Authors: Yates, L.A. / Durrant, B.P. / Fleurdepine, S. / Harlos, K. / Norbury, C.J. / Gilbert, R.J.C.
History
DepositionDec 7, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
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


Theoretical massNumber of molelcules
Total (without water)83,3272
Polymers83,3272
Non-polymers00
Water61334
1
A: POLY(A) RNA POLYMERASE PROTEIN CID1


Theoretical massNumber of molelcules
Total (without water)41,6631
Polymers41,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLY(A) RNA POLYMERASE PROTEIN CID1


Theoretical massNumber of molelcules
Total (without water)41,6631
Polymers41,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.800, 103.770, 76.390
Angle α, β, γ (deg.)90.00, 110.78, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein POLY(A) RNA POLYMERASE PROTEIN CID1 / CAFFEINE-INDUCED DEATH PROTEIN 1 / CAFFEINE-INDUCED DEATH SUPPRESSOR 1 URIDYLYLTRANSFERASE


Mass: 41663.445 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PGEX-6P-TCID1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O13833, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS PROTEIN HAS THE SURFACE ENTROPY REDUCTION MUTATIONS K133A R137A R277A K282A THIS PROTEIN HAS ...THIS PROTEIN HAS THE SURFACE ENTROPY REDUCTION MUTATIONS K133A R137A R277A K282A THIS PROTEIN HAS THE SURFACE ENTROPY REDUCTION MUTATIONS K133A R137A R277A K282A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 % / Description: NONE
Crystal growpH: 7 / Details: 20MM HEPES, 200MM NACL, 0.5MM TCEP, PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.52→58.83 Å / Num. obs: 30480 / % possible obs: 98.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 23
Reflection shellResolution: 2.52→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1772)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4E7X

4e7x


Resolution: 2.52→58.833 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2183 1538 5.05 %
Rwork0.1761 --
obs0.1782 30460 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→58.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5452 0 0 34 5486
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045585
X-RAY DIFFRACTIONf_angle_d0.8817553
X-RAY DIFFRACTIONf_dihedral_angle_d15.8452079
X-RAY DIFFRACTIONf_chiral_restr0.034827
X-RAY DIFFRACTIONf_plane_restr0.006966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.60140.32481580.27072574X-RAY DIFFRACTION99
2.6014-2.69430.31951290.26442634X-RAY DIFFRACTION99
2.6943-2.80220.30231350.24622703X-RAY DIFFRACTION100
2.8022-2.92980.30341300.23432651X-RAY DIFFRACTION99
2.9298-3.08420.28881270.2262641X-RAY DIFFRACTION99
3.0842-3.27740.27221380.21392659X-RAY DIFFRACTION99
3.2774-3.53040.24731520.20212626X-RAY DIFFRACTION99
3.5304-3.88570.21051350.17572594X-RAY DIFFRACTION97
3.8857-4.44780.191500.15112584X-RAY DIFFRACTION97
4.4478-5.6030.18071370.13722617X-RAY DIFFRACTION97
5.603-58.84880.17761470.14542639X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.66494.1318-3.03054.4308-3.85312.9807-0.2841-0.0686-0.754-0.0713-0.0386-0.84990.36440.07560.41020.61030.0348-0.00690.4450.04610.600166.0681-2.935728.4825
21.8272.3753.72883.60445.25268.65150.11690.1659-0.1226-0.1085-0.10130.35080.8266-0.5357-0.13130.7111-0.05250.1120.49430.0360.68651.6521-17.622735.57
39.1018-3.87363.00872.7588-3.31057.1026-0.0353-0.39950.7485-0.0218-0.1033-0.3154-0.13680.56950.11980.7981-0.08390.14440.455-0.05680.66556.3276-11.310540.0089
42.7390.47350.54423.7413-0.48093.0711-0.0058-0.15240.06210.45950.21140.4863-0.1217-0.5009-0.19410.49620.0620.08710.43290.09840.452752.266911.543422.8039
57.94434.62164.29393.79025.01878.48560.00710.04820.8188-0.4507-0.09650.4338-1.0078-0.50230.24030.79210.12860.07820.64170.05870.638670.385320.0576-0.4021
64.18651.13091.69318.9587.00366.0561-0.07950.0001-0.27070.3014-0.25120.20920.3972-0.60820.36740.672-0.09320.13090.58760.07260.433366.548-5.6281-8.3625
74.862.13483.36914.92372.12169.54770.1544-0.2079-0.09890.0359-0.0881-0.21990.46430.0084-0.11710.7079-0.04670.13580.49310.00740.543672.4303-12.0941-16.7542
84.21070.0788-0.47135.6291-1.49653.74620.21420.4298-0.0147-0.5519-0.0051-0.19040.0230.4552-0.16650.35530.00930.01290.5119-0.08440.368581.70017.3438-2.3508
93.7093-1.0356-0.44577.2272-0.8345.48540.1165-0.1757-0.20020.29710.1489-0.0760.47170.4041-0.27290.4669-0.0338-0.08120.5457-0.05080.314883.70974.68029.9542
103.4737-1.8001-1.71795.86011.89655.13640.14030.0065-0.0125-0.60640.0142-0.9957-0.01241.5652-0.15190.57880.00920.02591.063-0.06630.793499.73515.83470.5167
115.1033-2.8379-3.47514.79872.7722.5444-0.25030.8472-1.0373-1.19240.2739-0.23521.10290.5335-0.04970.95890.16290.02591.2052-0.23090.793895.5677-0.7364-9.5876
122.5719-3.5417-0.24998.2667-0.77014.62050.4260.95010.809-0.6803-0.3085-0.4591-1.05950.5117-0.23890.8409-0.10650.19840.89960.14070.818485.453124.2246-8.5392
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 41 THROUGH 101 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 102 THROUGH 127 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 128 THROUGH 165 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 166 THROUGH 381 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 41 THROUGH 58 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 59 THROUGH 101 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 102 THROUGH 165 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 166 THROUGH 224 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 225 THROUGH 280 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 281 THROUGH 312 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 313 THROUGH 343 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 344 THROUGH 382 )

+
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