6AHR

Cryo-EM structure of human Ribonuclease P


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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:  

  • 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 <sup>Val </sup>. Human RNase P is a large ...

    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.,Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.,CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Shanghai Institute of Precision Medicine, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China. Electronic address: pengfeilan@shsmu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonucleases P/MRP protein subunit POP1
B
1024Homo sapiensMutation(s): 0 
Gene Names: POP1 (KIAA0061)
EC: 3.1.26.5
Find proteins for Q99575 (Homo sapiens)
Go to Gene View: POP1
Go to UniProtKB:  Q99575
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p38
C
283Homo sapiensMutation(s): 0 
Gene Names: RPP38
EC: 3.1.26.5
Find proteins for P78345 (Homo sapiens)
Go to Gene View: RPP38
Go to UniProtKB:  P78345
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p29
D
220Homo sapiensMutation(s): 0 
Gene Names: POP4 (RPP29)
EC: 3.1.26.5
Find proteins for O95707 (Homo sapiens)
Go to Gene View: POP4
Go to UniProtKB:  O95707
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P/MRP protein subunit POP5
E
163Homo sapiensMutation(s): 0 
Gene Names: POP5
EC: 3.1.26.5
Find proteins for Q969H6 (Homo sapiens)
Go to Gene View: POP5
Go to UniProtKB:  Q969H6
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p25
F
199Homo sapiensMutation(s): 0 
Gene Names: RPP25
EC: 3.1.26.5
Find proteins for Q9BUL9 (Homo sapiens)
Go to Gene View: RPP25
Go to UniProtKB:  Q9BUL9
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p20
G
140Homo sapiensMutation(s): 0 
Gene Names: POP7 (RPP20)
EC: 3.1.26.5
Find proteins for O75817 (Homo sapiens)
Go to Gene View: POP7
Go to UniProtKB:  O75817
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p14
H
124Homo sapiensMutation(s): 0 
Gene Names: RPP14
EC: 3.1.26.5
Find proteins for O95059 (Homo sapiens)
Go to Gene View: RPP14
Go to UniProtKB:  O95059
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p30
I, J
268Homo sapiensMutation(s): 0 
Gene Names: RPP30 (RNASEP2)
EC: 3.1.26.5
Find proteins for P78346 (Homo sapiens)
Go to Gene View: RPP30
Go to UniProtKB:  P78346
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p21
K
154Homo sapiensMutation(s): 0 
Gene Names: RPP21 (C6orf135, CAT60)
EC: 3.1.26.5
Find proteins for Q9H633 (Homo sapiens)
Go to Gene View: RPP21
Go to UniProtKB:  Q9H633
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease P protein subunit p40
L
363Homo sapiensMutation(s): 0 
Gene Names: RPP40 (RNASEP1)
EC: 3.1.26.5
Find proteins for O75818 (Homo sapiens)
Go to Gene View: RPP40
Go to UniProtKB:  O75818
Entity ID: 1
MoleculeChainsLengthOrganism
H1 RNAA341Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
K
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-12-05
    Type: Initial release