Crystal Structure of Domain-Swapped Fam96a Major dimer

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

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The mammalian DUF59 protein Fam96a forms two distinct types of domain-swapped dimer.

Chen, K.E.Richards, A.A.Ariffin, J.K.Ross, I.L.Sweet, M.J.Kellie, S.Kobe, B.Martin, J.L.

(2012) Acta Crystallogr D Biol Crystallogr 68: 637-648

  • DOI: https://doi.org/10.1107/S0907444912006592
  • Primary Citation of Related Structures:  
    3UX2, 3UX3

  • PubMed Abstract: 

    Fam96a mRNA, which encodes a mammalian DUF59 protein, is enriched in macrophages. Recombinant human Fam96a forms stable monomers and dimers in solution. Crystal structures of these two forms revealed that each adopts a distinct type of domain-swapped dimer, one of which is stabilized by zinc binding. Two hinge loops control Fam96a domain swapping; both are flexible and highly conserved, suggesting that domain swapping may be a common feature of eukaryotic but not bacterial DUF59 proteins. The derived monomer fold of Fam96a diverges from that of bacterial DUF59 counterparts in that the C-terminal region of Fam96a is much longer and is positioned on the opposite side of the N-terminal core fold. The putative metal-binding site of bacterial DUF59 proteins is not conserved in Fam96a, but Fam96a interacts tightly in vitro with Ciao1, the cytosolic iron-assembly protein. Moreover, Fam96a and Ciao1 can be co-immunoprecipitated, suggesting that the interaction also occurs in vivo. Although predicted to have a signal peptide, it is shown that Fam96a is cytoplasmic. The data reveal that eukaryotic DUF59 proteins share intriguing characteristics with amyloidogenic proteins.

  • Organizational Affiliation

    Institute for Molecular Bioscience, Division of Chemistry and Structural Biology, University of Queensland, Brisbane, Queensland 4072, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MIP18 family protein FAM96A130Homo sapiensMutation(s): 0 
Gene Names: FAM96A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H5X1 (Homo sapiens)
Explore Q9H5X1 
Go to UniProtKB:  Q9H5X1
GTEx:  ENSG00000166797 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H5X1
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.411α = 90
b = 90.961β = 90
c = 34.69γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Advisory, Database references, Derived calculations