Crystal structure of mouse fetuin-B

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 

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Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition.

Cuppari, A.Korschgen, H.Fahrenkamp, D.Schmitz, C.Guevara, T.Karmilin, K.Kuske, M.Olf, M.Dietzel, E.Yiallouros, I.de Sanctis, D.Goulas, T.Weiskirchen, R.Jahnen-Dechent, W.Floehr, J.Stoecker, W.Jovine, L.Gomis-Ruth, F.X.

(2019) IUCrJ 6: 317-330

  • DOI: https://doi.org/10.1107/S2052252519001568
  • Primary Citation of Related Structures:  
    6HPV, 6HT9

  • PubMed Abstract: 

    Mammalian fetuin-A and fetuin-B are abundant serum proteins with pleiotropic functions. Fetuin-B is a highly selective and potent inhibitor of metallo-peptidases (MPs) of the astacin family, which includes ovastacin in mammals. By inhibiting ovastacin, fetuin-B is essential for female fertility. The crystal structure of fetuin-B was determined unbound and in complex with archetypal astacin, and it was found that the inhibitor has tandem cystatin-type modules (CY1 and CY2). They are connected by an exposed linker with a rigid, disulfide-linked 'CPDCP-trunk', and are followed by a C-terminal region (CTR) with little regular secondary structure. The CPDCP-trunk and a hairpin of CY2 form a bipartite wedge, which slots into the active-site cleft of the MP. These elements occupy the nonprimed and primed sides of the cleft, respectively, but spare the specificity pocket so that the inhibitor is not cleaved. The aspartate in the trunk blocks the catalytic zinc of astacin, while the CY2 hairpin binds through a QWV X GP motif. The CY1 module assists in structural integrity and the CTR is not involved in inhibition, as verified by in vitro studies using a cohort of mutants and variants. Overall, the inhibition conforms to a novel 'raised-elephant-trunk' mechanism for MPs, which is reminiscent of single-domain cystatins that target cysteine peptidases. Over 200 sequences from vertebrates have been annotated as fetuin-B, underpinning its ubiquity and physiological relevance; accordingly, sequences with conserved CPDCP- and QWV X GP-derived motifs have been found from mammals to cartilaginous fishes. Thus, the raised-elephant-trunk mechanism is likely to be generally valid for the inhibition of astacins by orthologs of fetuin-B.

  • Organizational Affiliation

    Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fetuin-B378Mus musculusMutation(s): 0 
Gene Names: Fetub
Find proteins for Q9QXC1 (Mus musculus)
Explore Q9QXC1 
Go to UniProtKB:  Q9QXC1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QXC1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.226 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.71α = 90
b = 67.71β = 90
c = 197.81γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXmodel building
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-03999
European Molecular Biology OrganizationGermany--
German Research Foundation--

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-03-27
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary