10CW | pdb_000010cw

Crystal structure of Thermoproteus neutrophilus Rpp30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 
    0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

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Ligand Structure Quality Assessment 


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Literature

Crystal structures of type T archaeal ribonuclease P Rpp30, Rpp30/Pop5, and L7Ae provide insights into a reduced RNase P.

Chan, C.W.Mondragon, A.

(2026) Nucleic Acids Res 54

  • DOI: https://doi.org/10.1093/nar/gkag792
  • Primary Citation Related Structures: 
    10CW, 10CX, 10CY, 10CZ, 10DA

  • PubMed Abstract: 

    RNase P is primarily responsible for processing the 5' end of precursor transfer RNA (tRNA). Although there are protein-only RNase P enzymes, the most widely distributed RNase Ps form ribonucleoprotein complexes where the number of protein components varies across evolutionary domains. Ribonucleoprotein RNase P enzymes universally contain a single RNA component. Pyrobaculum, a genus of archaeal hyperthermophiles, possess a minimal RNase P composed of a small RNA subunit and four small proteins. To understand the structure of this minimal RNase P, high-resolution structures of three protein components from Pyrobaculum were determined. These structures reveal that the proteins closely resemble their larger homologs, although entire secondary structure elements are absent in some instances. Modeling of the RNA subunit suggests a structure closely related to the RNA components of other RNase P complexes, but with a minimal S-domain containing only a single T-loop. The modeling further supports the formation of an RNase P complex that retains all the elements needed for tRNA recognition and processing. Finally, RNA composition analysis by size exclusion chromatography indicates that the L7Ae protein component may assist in the folding and structural stabilization of the RNA subunit.


  • Organizational Affiliation
    • Department of Molecular Biosciences, Northwestern University, 2205 Tech Drive, Evanston, IL 60208-3500, United States.

Macromolecule Content 

  • Total Structure Weight: 40.89 kDa 
  • Atom Count: 3,267 
  • Modeled Residue Count: 348 
  • Deposited Residue Count: 358 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ribonuclease P Rpp30
A, B
179Pyrobaculum neutrophilumMutation(s): 0 
Gene Names: Rpp30
UniProt
Find proteins for B1YD41 (Pyrobaculum neutrophilum (strain DSM 2338 / JCM 9278 / NBRC 100436 / V24Sta))
Explore B1YD41 
Go to UniProtKB:  B1YD41
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB1YD41
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free:  0.232 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.205 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.758α = 90
b = 66.368β = 113.81
c = 66.056γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
SHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35 GM118108
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM058443
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States4T32 GM008152
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5T32 GM008382

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-26
    Type: Initial release