[English] 日本語
Yorodumi
- PDB-7q72: Structure of Pla1 in complex with Red1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7q72
TitleStructure of Pla1 in complex with Red1
Components
  • NURS complex subunit red1
  • Poly(A) polymerase pla1
KeywordsTRANSFERASE / PolyA polymerase
Function / homology
Function and homology information


MTREC complex / cleavage body / nuclear exosome focus / sno(s)RNA processing / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of meiosis-specific transcripts / siRNA-independent facultative heterochromatin formation / nucleolar peripheral inclusion body / Mei2 nuclear dot complex / heterochromatin island ...MTREC complex / cleavage body / nuclear exosome focus / sno(s)RNA processing / nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of meiosis-specific transcripts / siRNA-independent facultative heterochromatin formation / nucleolar peripheral inclusion body / Mei2 nuclear dot complex / heterochromatin island / co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway / mRNA cleavage and polyadenylation specificity factor complex / polynucleotide adenylyltransferase / poly(A) RNA polymerase activity / regulatory ncRNA-mediated gene silencing / protein-macromolecule adaptor activity / nuclear body / chromatin / RNA binding / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol
Similarity search - Function
Putative zinc-finger domain / Putative zinc-finger domain / NURS complex subunit red1 / Poly(A) polymerase / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / : / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(A) polymerase nucleotidyltransferase domain ...Putative zinc-finger domain / Putative zinc-finger domain / NURS complex subunit red1 / Poly(A) polymerase / Poly(A) polymerase, RNA-binding domain / Poly(A) polymerase, central domain / : / Poly(A) polymerase predicted RNA binding domain / Poly(A) polymerase central domain / Poly(A) polymerase nucleotidyltransferase domain / Nucleotidyltransferase, class I-like, C-terminal / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Poly(A) polymerase pla1 / NURS complex subunit red1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsSoni, K. / Wild, K. / Sinning, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
CitationJournal: Nat Commun / Year: 2023
Title: Mechanistic insights into RNA surveillance by the canonical poly(A) polymerase Pla1 of the MTREC complex.
Authors: Soni, K. / Sivadas, A. / Horvath, A. / Dobrev, N. / Hayashi, R. / Kiss, L. / Simon, B. / Wild, K. / Sinning, I. / Fischer, T.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Poly(A) polymerase pla1
C: NURS complex subunit red1
B: Poly(A) polymerase pla1
D: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)146,0064
Polymers146,0064
Non-polymers00
Water543
1
A: Poly(A) polymerase pla1
C: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)73,0032
Polymers73,0032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-12 kcal/mol
Surface area27020 Å2
MethodPISA
2
B: Poly(A) polymerase pla1
D: NURS complex subunit red1


Theoretical massNumber of molelcules
Total (without water)73,0032
Polymers73,0032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-8 kcal/mol
Surface area24910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.644, 151.337, 65.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

-
Components

#1: Protein Poly(A) polymerase pla1 / PAP / Polynucleotide adenylyltransferase


Mass: 65380.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: pla1, SPBC646.04 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q10295, polynucleotide adenylyltransferase
#2: Protein NURS complex subunit red1


Mass: 7622.071 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: red1, iss3, SPAC1006.03c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UTR8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium formate, 20% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2021
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.8→98.017 Å / Num. obs: 20986 / % possible obs: 97.3 % / Redundancy: 13.164 % / Biso Wilson estimate: 51.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.1031 / Net I/σ(I): 9.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.89-2.9713.3654.3710.5827037212820230.4064.54695.1
2.97-3.0513.8393.7210.7627429203819820.513.86497.3
3.05-3.1413.8033.2070.8926585199519260.6143.3396.5
3.14-3.2313.6482.211.3425972196319030.7492.29796.9
3.23-3.3413.5971.8551.6524720189118180.7881.92896.1
3.34-3.4613.3861.4842.123265183417380.8811.54394.8
3.46-3.5913.431.1422.7622791178316970.9281.18895.2
3.59-3.7313.5780.6834.3722092168916270.9760.71196.3
3.73-3.913.5920.4246.5321883165616100.9880.44197.2
3.9-4.0913.3010.3088.7320550158015450.9940.32197.8
4.09-4.3113.1920.22511.1219353149114670.9940.23598.4
4.31-4.5713.0250.17713.3618313142414060.9970.18498.7
4.57-4.8912.7590.14615.7516868133213220.9970.15399.2
4.89-5.2812.5180.13916.5315623125812480.9970.14599.2
5.28-5.7812.5450.1317.2814552116811600.9950.13699.3
5.78-6.4712.8130.11619.5613620106710630.9970.12199.6
6.47-7.4712.1520.0923.25113389389330.9980.09499.5
7.47-9.1411.6770.06628.2694008128050.9980.06999.1
9.14-12.9311.5220.05932.0574436466460.9980.062100
12.93-98.0179.770.05929.237423893830.9920.06398.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.89 Å97.7 Å
Translation2.89 Å97.7 Å

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158+SVNrefinement
STARANISOdata scaling
XDSdata scaling
XDSdata reduction
PHASER2.8.0phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: deposition ID D_1292115151

Resolution: 2.8→98.017 Å / SU ML: 0.3699 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.8469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2835 1999 9.74 %
Rwork0.2407 18528 -
obs0.2448 20527 63.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→98.017 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8528 0 0 3 8531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00188732
X-RAY DIFFRACTIONf_angle_d0.466911865
X-RAY DIFFRACTIONf_chiral_restr0.04121339
X-RAY DIFFRACTIONf_plane_restr0.00371514
X-RAY DIFFRACTIONf_dihedral_angle_d20.0993240
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.5038440.3284410X-RAY DIFFRACTION20.17
2.88-2.950.3618510.3279464X-RAY DIFFRACTION22.82
2.95-3.040.4425550.3393518X-RAY DIFFRACTION25.7
3.04-3.140.3223630.3362579X-RAY DIFFRACTION28.03
3.14-3.250.3235750.326694X-RAY DIFFRACTION34.32
3.25-3.380.2866930.3043860X-RAY DIFFRACTION42.34
3.38-3.530.36561400.29851293X-RAY DIFFRACTION63.16
3.53-3.720.34591710.29181597X-RAY DIFFRACTION77.44
3.72-3.950.32181860.25251711X-RAY DIFFRACTION83.79
3.95-4.260.2962110.23141961X-RAY DIFFRACTION94.07
4.26-4.690.25212230.21572063X-RAY DIFFRACTION99.39
4.69-5.360.28562240.21412077X-RAY DIFFRACTION99.22
5.37-6.760.26752260.23612097X-RAY DIFFRACTION99.44
6.76-98.020.20712370.20152204X-RAY DIFFRACTION98.51

+
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