6AHV

Crystal structure of human RPP40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM Structure of the Human Ribonuclease P Holoenzyme.

Wu, J.Niu, S.Tan, M.Huang, C.Li, M.Song, Y.Wang, Q.Chen, J.Shi, S.Lan, P.Lei, M.

(2018) Cell 175: 1393-1404.e11

  • DOI: https://doi.org/10.1016/j.cell.2018.10.003
  • Primary Citation of Related Structures:  
    6AHR, 6AHU, 6AHV

  • PubMed 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 complex with tRNA Val . 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.


  • Organizational Affiliation

    Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p40363Homo sapiensMutation(s): 0 
Gene Names: RPP40RNASEP1
EC: 3.1.26.5
UniProt & NIH Common Fund Data Resources
Find proteins for O75818 (Homo sapiens)
Explore O75818 
Go to UniProtKB:  O75818
PHAROS:  O75818
GTEx:  ENSG00000124787 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75818
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.398α = 90
b = 129.892β = 90
c = 116.84γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-05
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Data collection, Database references