2ZAE

Crystal structure of protein Ph1601p in complex with protein Ph1771p of archaeal ribonuclease P from Pyrococcus horikoshii OT3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure of an archaeal homolog of the human protein complex Rpp21-Rpp29 that is a key core component for the assembly of active ribonuclease P.

Honda, T., Kakuta, Y., Kimura, K., Saho, J., Kimura, M.

(2008) J Mol Biol 384: 652-662

  • DOI: 10.1016/j.jmb.2008.09.056
  • Primary Citation of Related Structures:  
    2ZAE

  • PubMed Abstract: 

    • Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of the 5'-leader sequence of precursor tRNA. Human RNase P protein subunits Rpp21 and Rpp29, which bind to each other, with catalytic RNA (H1 RNA) are sufficient for activating endonucleolytic cleavage of precursor tRNA ...

    Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the processing of the 5'-leader sequence of precursor tRNA. Human RNase P protein subunits Rpp21 and Rpp29, which bind to each other, with catalytic RNA (H1 RNA) are sufficient for activating endonucleolytic cleavage of precursor tRNA. Here we have determined the crystal structure of the complex between the Pyrococcus horikoshii RNase P proteins PhoRpp21 and PhoRpp29, the archaeal homologs of Rpp21 and Rpp29, respectively. PhoRpp21 and PhoRpp29 form a heterodimeric structure where the two N-terminal helices (alpha1 and alpha2) in PhoRpp21 predominantly interact with the N-terminal extended structure, the beta-strand (beta2), and the C-terminal helix (alpha3) in PhoRpp29. The interface is dominated by hydrogen bonds and several salt bridges, rather than hydrophobic interactions. The electrostatic potential on the surface of the heterodimer shows a positively charged cluster on one face, suggesting a possible RNA-binding surface of the PhoRpp21-PhoRpp29 complex. The present structure, along with the result of a mutational analysis, suggests that heterodimerization between PhoRpp21 and PhoRpp29 plays an important role in the function of P. horikoshii RNase P.

    Organizational Affiliation: 

    Laboratory of Structural Biology, Graduate School of Systems Life Sciences, Kyushu University, Hakozaki 6-10-1, Fukuoka 812-8581, Japan.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein component 1A, C127Pyrococcus horikoshiiMutation(s): 0 
Gene Names: rnp1
EC: 3.1.26.5
Find proteins for O59425 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59425 
Go to UniProtKB:  O59425
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease P protein component 4B, D120Pyrococcus horikoshiiMutation(s): 0 
Gene Names: rnp4
EC: 3.1.26.5
Find proteins for O59248 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3))
Explore O59248 
Go to UniProtKB:  O59248
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download Ideal Coordinates CCD File 
 H [auth A], I [auth A], L [auth B], S [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
 J [auth B], P [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
NO3
Query on NO3
Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , K [auth B] , M [auth C] , N [auth C] , O [auth C] , Q [auth D] , 
E [auth A],  F [auth A],  G [auth A],  K [auth B],  M [auth C],  N [auth C],  O [auth C],  Q [auth D],  R [auth D]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.829α = 90
b = 127.07β = 90
c = 51.857γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance