6AHU

Cryo-EM structure of human Ribonuclease P with mature tRNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 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-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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonucleases P/MRP protein subunit POP11,024Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000104356 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p38283Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000152464 
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UniProt GroupP78345
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p29220Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000105171 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P/MRP protein subunit POP5163Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000167272 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p25199Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000178718 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p20140Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000172336 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p14124Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000163684 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p30
I, J
268Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000148688 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p21154Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000241370 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p40363Homo sapiensMutation(s): 0 
EC: 3.1.26.5
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GTEx:  ENSG00000124787 
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Entity ID: 1
MoleculeChains LengthOrganismImage
H1 RNA341Homo sapiens
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Entity ID: 12
MoleculeChains LengthOrganismImage
tRNAM [auth T]72Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
N [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.66 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: 2018-12-05
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Other
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references