Structure of the complete ABCE1/RNAase-L Inhibitor protein from Pyrococcus abysii

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 

Starting Model: experimental
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X-ray Structure of the Complete ABC Enzyme ABCE1 from Pyrococcus abyssi

Karcher, A.Schele, A.Hopfner, K.P.

(2008) J Biol Chem 283: 7962-7971

  • DOI: https://doi.org/10.1074/jbc.M707347200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The ATP binding cassette enzyme ABCE1 (also known as RNase-L (ribonuclease L) inhibitor, Pixie, and HP68), one of the evolutionary most sequence-conserved enzymes, functions in translation initiation, ribosome biogenesis, and human immunodeficiency virus capsid assembly. However, its structural mechanism and biochemical role in these processes have not been revealed. We determined the crystal structure of Pyrococcus abyssi ABCE1 in complex with Mg(2+) and ADP to 2.8A resolution. ABCE1 consists of four structural domains. Two nucleotide binding domains are arranged in a head-to-tail orientation by a hinge domain, suggesting that these domains undergo the characteristic tweezers-like powerstroke of ABC enzymes. In contrast to all other known ABC enzymes, ABCE1 has a N-terminal iron-sulfur-cluster (FeS) domain. The FeS domain contains two [4Fe-4S] clusters and is structurally highly related to bacterial-type ferredoxins. However, one cluster is coordinated by an unusual CX(4)CX(3/4)C triad. Surprisingly, intimate interactions of the FeS domain with the adenine and ribose binding Y-loop on nucleotide binding domain 1 suggest a linkage between FeS domain function and ATP-induced conformational control of the ABC tandem cassette. The structure substantially expands the functional architecture of ABC enzymes and raises the possibility that ABCE1 is a chemomechanical engine linked to a redox process.

  • Organizational Affiliation

    Center for Integrated Protein Science and Center for Advanced Photonics at the Gene Center, Ludwig-Maximilians-University Munich, D-81377 Munich, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ABC transporter ATP-binding protein607Pyrococcus abyssiMutation(s): 0 
Find proteins for Q9UZA4 (Pyrococcus abyssi (strain GE5 / Orsay))
Explore Q9UZA4 
Go to UniProtKB:  Q9UZA4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UZA4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.208 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.2α = 90
b = 63.2β = 90
c = 319.38γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Advisory, Refinement description
  • Version 1.3: 2023-11-01
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description