1IZ2

Interactions causing the kinetic trap in serpin protein folding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report



Literature

Interactions causing the kinetic trap in serpin protein folding

Im, H.Woo, M.-S.Hwang, K.Y.Yu, M.-H.

(2002) J Biol Chem 277: 46347-46354

  • DOI: 10.1074/jbc.M207682200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Conformational transition is fundamental to the mechanism of functional regulation in proteins, and serpins (serine protease inhibitors) can provide insight into this process. Serpins are metastable in their native forms, and they ordinarily undergo ...

    Conformational transition is fundamental to the mechanism of functional regulation in proteins, and serpins (serine protease inhibitors) can provide insight into this process. Serpins are metastable in their native forms, and they ordinarily undergo conformational transition to a stable state only when they form a tight complex with target proteases. The metastable native form is thus considered to be a kinetically trapped folding intermediate. We sought to understand the nature of the serpin kinetic trap as a step toward discovering how conformational transition is regulated. We found that mutations of the B/C beta-barrel of native alpha(1)-antitrypsin, a prototypical serpin, allowed conversion of the molecule into a more stable state. A 2.2 A resolution crystal structure of the stable form (PDB code, ) showed that the reactive site loop is inserted into an A beta-sheet, as in the latent plasminogen activator inhibitor-1. Mutational analyses suggest strongly that interactions not found in the final stable form cause the kinetic trap in serpin protein folding.


    Organizational Affiliation

    National Creative Research Initiatives, Protein Strain Research Center, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
alpha1-antitrypsinA394Homo sapiensMutation(s): 10 
Gene Names: SERPINA1AATPIPRO0684PRO2209
Find proteins for P01009 (Homo sapiens)
Explore P01009 
Go to UniProtKB:  P01009
NIH Common Fund Data Resources
PHAROS  P01009
Protein Feature View
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  • Reference Sequence
Oligosaccharides
Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
alpha-D-glucopyranose-(1-2)-(5R)-5-[(2R)-2-hydroxynonyl]-beta-D-xylulofuranose
B
2 N/A N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.02α = 90
b = 74.173β = 90
c = 93.115γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary