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 1.1 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: 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 ...

    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; Key laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201204, China. Electronic address: leim@shsmu.edu.cn.



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonucleases P/MRP protein subunit POP1B1024Homo sapiensMutation(s): 0 
Gene Names: POP1KIAA0061
EC: 3.1.26.5
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p38C283Homo sapiensMutation(s): 0 
Gene Names: RPP38
EC: 3.1.26.5
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p29D220Homo sapiensMutation(s): 0 
Gene Names: POP4RPP29
EC: 3.1.26.5
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P/MRP protein subunit POP5E163Homo sapiensMutation(s): 0 
Gene Names: POP5AD-008HSPC004x0003
EC: 3.1.26.5
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p25F199Homo sapiensMutation(s): 0 
Gene Names: RPP25
EC: 3.1.26.5
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p20G140Homo sapiensMutation(s): 0 
Gene Names: POP7RPP20
EC: 3.1.26.5
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p14H124Homo sapiensMutation(s): 0 
Gene Names: RPP14
EC: 3.1.26.5
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p30I, J268Homo sapiensMutation(s): 0 
Gene Names: RPP30RNASEP2
EC: 3.1.26.5
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p21K154Homo sapiensMutation(s): 0 
Gene Names: RPP21C6orf135CAT60
EC: 3.1.26.5
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein subunit p40L363Homo sapiensMutation(s): 0 
Gene Names: RPP40RNASEP1
EC: 3.1.26.5
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Entity ID: 1
MoleculeChainsLengthOrganismImage
H1 RNAA 341Homo sapiens
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Entity ID: 12
MoleculeChainsLengthOrganismImage
tRNAM [auth T]72Homo sapiens
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
N [auth K]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
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