5AWF

Crystal structure of SufB-SufC-SufD complex from Escherichia coli

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis

Hirabayashi, K., Yuda, E., Tanaka, N., Katayama, S., Iwasaki, K., Matsumoto, T., Kurisu, G., Outten, F.W., Fukuyama, K., Takahashi, Y., Wada, K.

(2015) J Biol Chem 290: 29717-29731

  • DOI: 10.1074/jbc.M115.680934
  • Primary Citation of Related Structures:  
    5AWF, 5AWG

  • PubMed Abstract: 

    • ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis ...

    ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD complex.

    Organizational Affiliation: 

    the Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan, keiwada@med.miyazaki-u.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FeS cluster assembly protein SufB A, E495Escherichia coli K-12Mutation(s): 0 
Gene Names: sufB, ynhE, b1683, JW5273
Find proteins for P77522 (Escherichia coli (strain K12))
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Go to UniProtKB:  P77522
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FeS cluster assembly protein SufD B, F423Escherichia coli K-12Mutation(s): 0 
Gene Names: sufD, ynhC, b1681, JW1671
Find proteins for P77689 (Escherichia coli (strain K12))
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Go to UniProtKB:  P77689
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent transporter SufC C, D, G, H248Escherichia coli K-12Mutation(s): 0 
Gene Names: sufC, ynhD, b1682, JW1672
Find proteins for P77499 (Escherichia coli (strain K12))
Explore P77499 
Go to UniProtKB:  P77499
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.475α = 90
b = 139.556β = 113.1
c = 124.684γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
Cootmodel building
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-11
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2020-02-26
    Changes: Data collection, Database references, Derived calculations