Experimental Data Snapshot

  • Resolution: 3.49 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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This is version 2.0 of the entry. See complete history


Crystal Structure of the Native Plasminogen Reveals an Activation-Resistant Compact Conformation.

Xue, Y.Bodin, C.Olsson, K.

(2012) J Thromb Haemost 10: 1385

  • DOI: https://doi.org/10.1111/j.1538-7836.2012.04765.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Plasminogen is the zymogen form of plasmin and the precursor of angiostatin. It has been implicated in a variety of disease states, including thrombosis, bleeding and cancers. The native plasminogen, known as Glu-plasminogen, contains seven domains comprising the N-terminal peptide domain (NTP), five kringle domains (K1-K5) and the C-terminal serine protease domain (SP). Previous studies have established that the lysine binding site (LBS) of the conserved kringle domains plays a crucial role in mediating the regulation of plasminogen function. However, details of the related conformational mechanism are unknown. We aim to understand in more detail the conformational mechanism of plasminogen activation involving the kringles. We crystallized the native plasminogen under physiologically relevant conditions and determined the structure at 3.5 Å resolution. We performed structural analyses and related these to the literature data to gain critical understanding of the plasminogen activation. The structure reveals the precise architecture of the quaternary complex. It shows that the Glu-plasminogen renders its compact form as an activation-resistant conformation for the proteolytic activation. The LBSs of all kringles, except K1, are engaged in intra-molecular interactions while only K1-LBS is readily available for ligand binding or receptor anchorage. The structure also provides insights into the interactions between plasminogen and α2-antiplasmin, the primary physiological inhibitor of plasmin. Furthermore, the data presented explain why a conformational transition to the open form is necessary for plasminogen activation as well as angiostatin generation, and provide a rationale for the functional hierarchy of the different kringles.

  • Organizational Affiliation

    Discovery Sciences, AstraZeneca R&D Mölndal, Mölndal, Sweden. yafeng.xue@astrazeneca.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PLASMINOGENA [auth S]791Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens)
Explore P00747 
Go to UniProtKB:  P00747
GTEx:  ENSG00000122194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00747
Glycosylation Sites: 1Go to GlyGen: P00747-1
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranoseB [auth A]3O-Glycosylation
Glycosylation Resources
GlyTouCan:  G02684WR
GlyCosmos:  G02684WR
GlyGen:  G02684WR
Experimental Data & Validation

Experimental Data

  • Resolution: 3.49 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.46α = 90
b = 118.46β = 90
c = 179.25γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Other
  • Version 1.2: 2012-07-18
    Changes: Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary