[English] 日本語
Yorodumi
- PDB-6ahu: Cryo-EM structure of human Ribonuclease P with mature tRNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ahu
TitleCryo-EM structure of human Ribonuclease P with mature tRNA
Components
  • (Ribonuclease P protein subunit ...) x 8
  • H1 RNA
  • Ribonuclease P/MRP protein subunit POP5
  • Ribonucleases P/MRP protein subunit POP1
  • tRNA
KeywordsHYDROLASE/RNA / Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex
Function / homology
Function and homology information


multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing ...multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing / centriolar satellite / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / fibrillar center / rRNA processing / response to xenobiotic stimulus / intracellular membrane-bounded organelle / nucleolus / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease P protein subunit Rpp38 / POP1 C-terminal domain / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / : / Pop1, N-terminal / POPLD domain / Ribonuclease P/MRP protein subunit Pop5 / Ribonucleases P/MRP protein subunit Pop1 / : ...Ribonuclease P protein subunit Rpp38 / POP1 C-terminal domain / Ribonuclease P protein subunit Rpp40 / Ribonuclease P 40kDa (Rpp40) subunit / : / 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 / 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. / DNA/RNA-binding protein Alba-like / Alba / Rof/RNase P-like / Alba-like domain superfamily / Polymerase/histidinol phosphatase-like / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
: / : / RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P protein subunit p20 / Ribonuclease P protein subunit p40 / Ribonuclease P protein subunit p14 / Ribonuclease P protein subunit p29 / Ribonuclease P protein subunit p38 ...: / : / RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P protein subunit p20 / Ribonuclease P protein subunit p40 / Ribonuclease P protein subunit p14 / Ribonuclease P protein subunit p29 / Ribonuclease P protein subunit p38 / Ribonuclease P protein subunit p30 / Ribonuclease P/MRP protein subunit POP5 / Ribonucleases P/MRP protein subunit POP1 / Ribonuclease P protein subunit p25 / Ribonuclease P protein subunit p21
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsWu, J. / Niu, S. / Tan, M. / Lan, P. / Lei, M.
CitationJournal: Cell / Year: 2018
Title: Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.
Authors: Jian Wu / Shuangshuang Niu / Ming Tan / Chenhui Huang / Mingyue Li / Yang Song / Qianmin Wang / Juan Chen / Shaohua Shi / Pengfei Lan / Ming Lei /
Abstract: Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in ...Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in complex with tRNA. Human RNase P is a large ribonucleoprotein complex that contains 10 protein components and one catalytic RNA. The protein components form an interlocked clamp that stabilizes the RNA in a conformation optimal for substrate binding. Human RNase P recognizes the tRNA using a double-anchor mechanism through both protein-RNA and RNA-RNA interactions. Structural comparison of the apo and tRNA-bound human RNase P reveals that binding of tRNA induces a local conformational change in the catalytic center, transforming the ribozyme into an active state. Our results also provide an evolutionary model depicting how auxiliary RNA elements in bacterial RNase P, essential for substrate binding, and catalysis, were replaced by the much more complex and multifunctional protein components in higher organisms.
History
DepositionAug 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
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-9627
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H1 RNA
B: Ribonucleases P/MRP protein subunit POP1
C: Ribonuclease P protein subunit p38
D: Ribonuclease P protein subunit p29
E: Ribonuclease P/MRP protein subunit POP5
F: Ribonuclease P protein subunit p25
G: Ribonuclease P protein subunit p20
H: Ribonuclease P protein subunit p14
I: Ribonuclease P protein subunit p30
J: Ribonuclease P protein subunit p30
K: Ribonuclease P protein subunit p21
L: Ribonuclease P protein subunit p40
T: tRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)492,83414
Polymers492,76913
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area65880 Å2
ΔGint-428 kcal/mol
Surface area173340 Å2

-
Components

-
RNA chain , 2 types, 2 molecules AT

#1: RNA chain H1 RNA


Mass: 110244.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: GenBank: 31969
#12: RNA chain tRNA


Mass: 23168.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: in vitro transcription / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGlms / Production host: Homo sapiens (human) / References: GenBank: 3217024

-
Protein , 2 types, 2 molecules BE

#2: Protein Ribonucleases P/MRP protein subunit POP1 / hPOP1


Mass: 114896.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q99575, ribonuclease P
#5: Protein Ribonuclease P/MRP protein subunit POP5 / hPop5


Mass: 18844.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q969H6, ribonuclease P

-
Ribonuclease P protein subunit ... , 8 types, 9 molecules CDFGHIJKL

#3: Protein Ribonuclease P protein subunit p38 / RNaseP protein p38


Mass: 31891.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P78345, ribonuclease P
#4: Protein Ribonuclease P protein subunit p29 / hPOP4


Mass: 25474.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O95707, ribonuclease P
#6: Protein Ribonuclease P protein subunit p25 / RNase P protein subunit p25


Mass: 20659.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BUL9, ribonuclease P
#7: Protein Ribonuclease P protein subunit p20 / RNaseP protein p20 / Ribonucleases P/MRP protein subunit POP7 homolog / hPOP7


Mass: 15672.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O75817, ribonuclease P
#8: Protein Ribonuclease P protein subunit p14


Mass: 13707.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O95059, ribonuclease P
#9: Protein Ribonuclease P protein subunit p30 / RNaseP protein p30 / RNase P subunit 2


Mass: 29364.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: P78346, ribonuclease P
#10: Protein Ribonuclease P protein subunit p21 / RNaseP protein p21 / Ribonuclease P/MRP 21 kDa subunit / Ribonucleoprotein V


Mass: 17596.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: Q9H633, ribonuclease P
#11: Protein Ribonuclease P protein subunit p40 / RNaseP protein p40 / RNase P subunit 1


Mass: 41884.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) Homo sapiens (human) / References: UniProt: O75818, ribonuclease P

-
Non-polymers , 1 types, 1 molecules

#13: Chemical ChemComp-ZN / ZINC ION


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

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1RNase P with tRNACOMPLEX#1-#120MULTIPLE SOURCES
2RNase PCOMPLEX#1-#111NATURAL
3RNACOMPLEX#121RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Homo sapiens (human)9606
23Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human) / Plasmid: pGlms
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: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287700 / 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