High resolution structure of Methanocaldococcus jannaschii L7AE

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.135 

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This is version 1.4 of the entry. See complete history


The Crystal Structure of the Methanocaldococcus jannaschii Multifunctional L7Ae RNA-Binding Protein Reveals an Induced-Fit Interaction with the Box C/D RNAs.

Suryadi, J.Tran, E.J.Maxwell, E.S.Brown II, B.A.

(2005) Biochemistry 44: 9657-9672

  • DOI: https://doi.org/10.1021/bi050568q
  • Primary Citation of Related Structures:  
    1RA4, 1XBI

  • PubMed Abstract: 

    Archaeal ribosomal protein L7Ae is a multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal, box H/ACA, and box C/D sRNAs. The crystal structure of Methanocaldococcus jannaschii L7Ae has been determined to 1.45 A, and L7Ae's amino acid composition, evolutionary conservation, functional characteristics, and structural details have been analyzed. Comparison of the L7Ae structure to those of a number of related proteins with diverse functions has revealed significant structural homology which suggests that this protein fold is an ancient RNA-binding motif. Notably, the free M. jannaschii L7Ae structure is essentially identical to that with RNA bound, suggesting that RNA binding occurs through an induced-fit interaction. Circular dichroism experiments show that box C/D and C'/D' RNA motifs undergo conformational changes when magnesium or the L7Ae protein is added, corroborating the induced-fit model for L7Ae-box C/D RNA interactions.

  • Organizational Affiliation

    Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7Ae120Methanocaldococcus jannaschiiMutation(s): 0 
Gene Names: RPL7AEMJ1203
Find proteins for P54066 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore P54066 
Go to UniProtKB:  P54066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54066
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on EPE

Download Ideal Coordinates CCD File 
C8 H18 N2 O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.132 
  • R-Value Observed: 0.135 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.665α = 90
b = 48.869β = 90
c = 51.914γ = 90
Software Package:
Software NamePurpose
MADNESSdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-09
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description