2VH4

Structure of a loop C-sheet serpin polymer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Structural Basis for Loop C-Sheet Polymerization in Serpins.

Zhang, Q.Law, R.H.Bottomley, S.P.Whisstock, J.C.Buckle, A.M.

(2008) J Mol Biol 376: 1348

  • DOI: https://doi.org/10.1016/j.jmb.2007.12.050
  • Primary Citation of Related Structures:  
    2VH4

  • PubMed Abstract: 

    In this study, we report the X-ray crystal structure of an N-terminally truncated variant of the bacterial serpin, tengpin (tengpinDelta42). Our data reveal that tengpinDelta42 adopts a variation of the latent conformation in which the reactive center loop is hyperinserted into the A beta-sheet and removed from the vicinity of the C-sheet. This conformational change leaves the C beta-sheet completely exposed and permits antiparallel edge-strand interactions between the exposed portion of the reactive center loop of one molecule and strand s2C of the C beta-sheet of the neighboring molecule in the crystal lattice. Our structural data thus reveal that tengpinDelta42 forms a loop C-sheet polymer in the crystal lattice. In vivo serpins have a propensity to misfold and form long-chain polymers, a process that underlies serpinopathies such as emphysema, thrombosis and dementia. Native serpins are thought to polymerize via a loop A-sheet mechanism. However, studies on plasminogen activator inhibitor 1 and the S49P variant of human neuroserpin reveal that the latent form of these molecules can also polymerize. Polymerization of latent neuroserpin may be important for the development of familial encephalopathy with neuroserpin inclusion bodies. Our structural data provide a possible mechanism for polymerization by latent serpins.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC 3800, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TENGPIN
A, B
381Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 0 
UniProt
Find proteins for Q8R9P5 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8R9P5 
Go to UniProtKB:  Q8R9P5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8R9P5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.895α = 90
b = 68.669β = 93.45
c = 137.651γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2017-07-12
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description