[English] 日本語
Yorodumi
- PDB-7y18: Crystal structure of ribosomal ITS2 pre-rRNA processing complex f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y18
TitleCrystal structure of ribosomal ITS2 pre-rRNA processing complex from Saccharomyces cerevisiae
Components
  • Polynucleotide 5'-hydroxyl-kinase GRC3
  • Protein LAS1
KeywordsRNA BINDING PROTEIN / RNA processing / Nuclease
Function / homology
Function and homology information


polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / nucleolar chromatin / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / termination of RNA polymerase I transcription / Major pathway of rRNA processing in the nucleolus and cytosol / preribosome, large subunit precursor / RNA processing ...polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / nucleolar chromatin / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / termination of RNA polymerase I transcription / Major pathway of rRNA processing in the nucleolus and cytosol / preribosome, large subunit precursor / RNA processing / maturation of LSU-rRNA / rRNA processing / endonuclease activity / phosphorylation / nucleolus / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
Las1 / Las1-like / Polyribonucleotide 5'-hydroxyl-kinase Clp1, P-loop domain / Polyribonucleotide 5-hydroxyl-kinase Clp1/Grc3 / mRNA cleavage and polyadenylation factor CLP1 P-loop / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Protein LAS1 / Polynucleotide 5'-hydroxyl-kinase GRC3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å
AuthorsChen, J. / Liu, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171286 China
CitationJournal: Elife / Year: 2024
Title: Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery.
Authors: Jiyun Chen / Hong Chen / Shanshan Li / Xiaofeng Lin / Rong Hu / Kaiming Zhang / Liang Liu /
Abstract: Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a ...Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length and Las1-Grc3 complexes, and Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis.
History
DepositionJun 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jan 17, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Polynucleotide 5'-hydroxyl-kinase GRC3
C: Protein LAS1
D: Protein LAS1
B: Polynucleotide 5'-hydroxyl-kinase GRC3
E: Polynucleotide 5'-hydroxyl-kinase GRC3
F: Protein LAS1


Theoretical massNumber of molelcules
Total (without water)395,3336
Polymers395,3336
Non-polymers00
Water3,243180
1
A: Polynucleotide 5'-hydroxyl-kinase GRC3
C: Protein LAS1
D: Protein LAS1
B: Polynucleotide 5'-hydroxyl-kinase GRC3


Theoretical massNumber of molelcules
Total (without water)263,5564
Polymers263,5564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22020 Å2
ΔGint-93 kcal/mol
Surface area87910 Å2
MethodPISA
2
E: Polynucleotide 5'-hydroxyl-kinase GRC3
F: Protein LAS1

E: Polynucleotide 5'-hydroxyl-kinase GRC3
F: Protein LAS1


Theoretical massNumber of molelcules
Total (without water)263,5564
Polymers263,5564
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area19360 Å2
ΔGint-99 kcal/mol
Surface area88080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)233.556, 116.142, 159.311
Angle α, β, γ (deg.)90.000, 96.406, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11F-605-

HOH

-
Components

#1: Protein Polynucleotide 5'-hydroxyl-kinase GRC3 / Protein GRC3


Mass: 72342.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: GRC3, YLL035W / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: Q07845, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
#2: Protein Protein LAS1


Mass: 59435.332 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c / Gene: LAS1, YKR063C / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P36146
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 2% tacsimate, pH 7.0, 0.1 M imidazole, pH 7.0, 2% 2-propanole, and 9% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 36773 / % possible obs: 98.8 % / Redundancy: 4.5 % / Biso Wilson estimate: 43.42 Å2 / Rpim(I) all: 0.157 / Net I/σ(I): 4.8
Reflection shellResolution: 3.5→3.56 Å / Num. unique obs: 2594 / Rpim(I) all: 0.585

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-30007.21data scaling
HKL-30007.21data reduction
Coot0.7.2.1model building
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OF4

6of4


Resolution: 3.69→48.63 Å / SU ML: 0.5523 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.5715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3179 1824 4.96 %
Rwork0.2784 34949 -
obs0.2803 36773 80.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.96 Å2
Refinement stepCycle: LAST / Resolution: 3.69→48.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22862 0 0 180 23042
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008223433
X-RAY DIFFRACTIONf_angle_d1.490131827
X-RAY DIFFRACTIONf_chiral_restr0.24523509
X-RAY DIFFRACTIONf_plane_restr0.00574047
X-RAY DIFFRACTIONf_dihedral_angle_d29.01338504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.69-3.790.926810.381137X-RAY DIFFRACTION1.08
3.79-3.90.355340.2845671X-RAY DIFFRACTION20.13
3.9-4.020.35041100.28011849X-RAY DIFFRACTION55.88
4.03-4.170.32881560.27452779X-RAY DIFFRACTION83.29
4.17-4.340.31161730.27613089X-RAY DIFFRACTION93.09
4.34-4.530.30731530.26813164X-RAY DIFFRACTION94.91
4.53-4.770.31111720.26473284X-RAY DIFFRACTION97.74
4.77-5.070.31971540.26963272X-RAY DIFFRACTION97.75
5.07-5.460.33631810.273315X-RAY DIFFRACTION98.78
5.46-6.010.33371730.3033307X-RAY DIFFRACTION98.86
6.01-6.880.351610.32643372X-RAY DIFFRACTION99.52
6.88-8.660.3061740.28873384X-RAY DIFFRACTION99.8
8.66-48.630.28361820.26373426X-RAY DIFFRACTION99.42

+
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