6K0B

cryo-EM structure of archaeal Ribonuclease P with mature tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme.

Wan, F.Wang, Q.Tan, J.Tan, M.Chen, J.Shi, S.Lan, P.Wu, J.Lei, M.

(2019) Nat Commun 10: 2617-2617

  • DOI: https://doi.org/10.1038/s41467-019-10496-3
  • Primary Citation of Related Structures:  
    6K0A, 6K0B

  • PubMed Abstract: 

    Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5' maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in complex with a tRNA substrate at resolutions of 4.6 Å and 4.3 Å, respectively. The structures reveal that the subunits of MjaRNase P are strung together to organize the holoenzyme in a dimeric conformation required for efficient catalysis. The structures also show that archaeal RNase P is a functional chimera of bacterial and eukaryal RNase Ps that possesses bacterial-like two RNA-based anchors and a eukaryal-like protein-aided stabilization mechanism. The 3'-RCCA sequence of tRNA, which is a key recognition element for bacterial RNase P, is dispensable for tRNA recognition by MjaRNase P. The overall organization of MjaRNase P, particularly within the active site, is similar to those of bacterial and eukaryal RNase Ps, suggesting a universal catalytic mechanism for all RNase Ps.


  • Organizational Affiliation

    Shanghai Institute of Precision Medicine, Shanghai, 200125, China. pengfeilan@shsmu.edu.cn.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein component 2A,
H [auth B]
134Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rnp2MJ0494
EC: 3.1.26.5
UniProt
Find proteins for Q57917 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Go to UniProtKB:  Q57917
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UniProt GroupQ57917
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein component 3B [auth C],
I [auth D]
232Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rnp3MJ1139
EC: 3.1.26.5
UniProt
Find proteins for Q58539 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein component 1C [auth E],
J [auth F]
95Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rnp1MJ0464
EC: 3.1.26.5
UniProt
Find proteins for Q57903 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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UniProt GroupQ57903
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein component 4D [auth G],
K [auth H]
128Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rnp4MJ0962
EC: 3.1.26.5
UniProt
Find proteins for Q58372 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeE [auth I],
L [auth J]
117Methanocaldococcus jannaschii DSM 2661Mutation(s): 0 
Gene Names: rpl7aeMJ1203
UniProt
Find proteins for P54066 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
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Entity ID: 6
MoleculeChains LengthOrganismImage
tRNAF [auth U],
M [auth V]
83Escherichia coli
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Entity ID: 7
MoleculeChains LengthOrganismImage
RPRG [auth X],
N [auth Y]
258Methanocaldococcus jannaschii
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-06
    Changes: Data collection, Other