[English] 日本語
Yorodumi
- PDB-7c79: Cryo-EM structure of yeast Ribonuclease MRP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c79
TitleCryo-EM structure of yeast Ribonuclease MRP
Components
  • (Ribonuclease MRP protein subunit ...) x 2
  • (Ribonuclease P/MRP protein subunit ...) x 2
  • (Ribonucleases P/MRP protein subunit ...) x 5
  • RNases MRP/P 32.9 kDa subunit
  • Ribonuclease MRP RNA subunit NME1
KeywordsRNA BINDING PROTEIN / Ribonuclease MRP / RNA-protein complex
Function / homology
Function and homology information


ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity ...ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / mRNA processing / rRNA processing / nucleolus / RNA binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Ribonuclease MRP protein subunit RMP1 / RNase P, subunit Pop3 / RNase P subunit Pop3 / Ribonucleases P/MRP protein subunit Pop8 / : / Ribonucleases P/MRP protein subunit Pop8 / Ribonuclease P/MRP subunit Pop7, fungi / Pop1, N-terminal ...: / : / Ribonuclease MRP protein subunit RMP1 / RNase P, subunit Pop3 / RNase P subunit Pop3 / Ribonucleases P/MRP protein subunit Pop8 / : / Ribonucleases P/MRP protein subunit Pop8 / Ribonuclease P/MRP subunit Pop7, fungi / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / : / Ribonucleases P/MRP protein subunit POP1, N-terminal / POPLD (NUC188) domain / POP1 C-terminal domain / Ribonucleases P/MRP protein subunit Rpp20/Pop7 / Rpp20 subunit of nuclear RNase MRP and P / RNase P subunit Pop5/Rpp14/Rnp2-like / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit p30 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Alba-like domain / Rof/RNase P-like / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like / Translation Initiation Factor IF3 / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP8 / Ribonucleases P/MRP protein subunit POP7 / RNases MRP/P 32.9 kDa subunit / Ribonuclease P/MRP protein subunit RPP1 / Ribonuclease MRP protein subunit SNM1 / Ribonucleases P/MRP protein subunit POP1 ...RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP8 / Ribonucleases P/MRP protein subunit POP7 / RNases MRP/P 32.9 kDa subunit / Ribonuclease P/MRP protein subunit RPP1 / Ribonuclease MRP protein subunit SNM1 / Ribonucleases P/MRP protein subunit POP1 / Ribonucleases P/MRP protein subunit POP6 / Ribonucleases P/MRP protein subunit POP3 / Ribonuclease MRP protein subunit RMP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Saccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsLan, P. / Wu, J. / Lei, M.
CitationJournal: Science / Year: 2020
Title: Structural insight into precursor ribosomal RNA processing by ribonuclease MRP.
Authors: Pengfei Lan / Bin Zhou / Ming Tan / Shaobai Li / Mi Cao / Jian Wu / Ming Lei /
Abstract: Ribonuclease (RNase) MRP is a conserved eukaryotic ribonucleoprotein complex that plays essential roles in precursor ribosomal RNA (pre-rRNA) processing and cell cycle regulation. In contrast to ...Ribonuclease (RNase) MRP is a conserved eukaryotic ribonucleoprotein complex that plays essential roles in precursor ribosomal RNA (pre-rRNA) processing and cell cycle regulation. In contrast to RNase P, which selectively cleaves transfer RNA-like substrates, it has remained a mystery how RNase MRP recognizes its diverse substrates. To address this question, we determined cryo-electron microscopy structures of RNase MRP alone and in complex with a fragment of pre-rRNA. These structures and the results of biochemical studies reveal that coevolution of both protein and RNA subunits has transformed RNase MRP into a distinct ribonuclease that processes single-stranded RNAs by recognizing a short, loosely defined consensus sequence. This broad substrate specificity suggests that RNase MRP may have myriad yet unrecognized substrates that could play important roles in various cellular contexts.
History
DepositionMay 24, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-30296
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease MRP RNA subunit NME1
B: Ribonucleases P/MRP protein subunit POP1
C: Ribonucleases P/MRP protein subunit POP3
D: RNases MRP/P 32.9 kDa subunit
E: Ribonuclease P/MRP protein subunit POP5
F: Ribonucleases P/MRP protein subunit POP6
G: Ribonucleases P/MRP protein subunit POP7
H: Ribonucleases P/MRP protein subunit POP8
I: Ribonuclease P/MRP protein subunit RPP1
J: Ribonuclease P/MRP protein subunit RPP1
K: Ribonuclease MRP protein subunit SNM1
L: Ribonuclease MRP protein subunit RMP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,02114
Polymers444,93112
Non-polymers902
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area60590 Å2
ΔGint-390 kcal/mol
Surface area159030 Å2

-
Components

-
Ribonucleases P/MRP protein subunit ... , 5 types, 5 molecules BCFGH

#2: Protein Ribonucleases P/MRP protein subunit POP1 / RNA-processing protein POP1 / RNases P/MRP 100.4 kDa subunit


Mass: 100559.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P41812, ribonuclease P
#3: Protein Ribonucleases P/MRP protein subunit POP3 / RNA-processing protein POP3 / RNases MRP/P 22.6 kDa subunit


Mass: 22643.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53833
#6: Protein Ribonucleases P/MRP protein subunit POP6 / RNA-processing protein POP6 / RNases P/MRP 18.2 kDa subunit


Mass: 18234.959 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P53218, ribonuclease P
#7: Protein Ribonucleases P/MRP protein subunit POP7 / RNA-processing protein POP7 / RNases P/MRP 15.8 kDa subunit


Mass: 15844.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38291, ribonuclease P
#8: Protein Ribonucleases P/MRP protein subunit POP8 / RNA-processing protein POP8 / RNases P/MRP 15.5 kDa subunit


Mass: 15530.351 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38208, ribonuclease P

-
Ribonuclease P/MRP protein subunit ... , 2 types, 3 molecules EIJ

#5: Protein Ribonuclease P/MRP protein subunit POP5 / RNA-processing protein POP5 / RNase P/MRP 19.6 kDa subunit


Mass: 19601.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P28005, ribonuclease P
#9: Protein Ribonuclease P/MRP protein subunit RPP1 / RNA-processing protein RPP1 / RNaseP/MRP 32.2 kDa subunit


Mass: 32270.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38786, ribonuclease P

-
Ribonuclease MRP protein subunit ... , 2 types, 2 molecules KL

#10: Protein Ribonuclease MRP protein subunit SNM1 / RNA-processing protein SNM1 / RNase MRP 22.5 kDa subunit


Mass: 22578.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40993
#11: Protein Ribonuclease MRP protein subunit RMP1 / RNA-processing protein RMP1 / RNase MRP 23.6 kDa subunit


Mass: 23657.668 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12530

-
RNA chain / Protein , 2 types, 2 molecules AD

#1: RNA chain Ribonuclease MRP RNA subunit NME1


Mass: 108806.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Saccharomyces cerevisiae S288C (yeast)
#4: Protein RNases MRP/P 32.9 kDa subunit / RNA-processing protein POP4


Mass: 32933.168 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P38336

-
Non-polymers , 2 types, 2 molecules

#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#13: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Ribonuclease MRP / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: s288c
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1232761 / Symmetry type: POINT

+
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