Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 88.54 kDa 
• Atom Count: 5317 
• Modelled Residue Count: 682 
• Deposited Residue Count: 791 
• Unique protein chains: 1

4DUU

The X-ray Crystal Structure of Full-Length type I Human Plasminogen

• PDB DOI: 10.2210/pdb4DUU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2012-02-22 Released: 2012-03-28 
• Deposition Author(s): Law, R.H.P., Caradoc-Davies, T., Whisstock, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.20 Å
• R-Value Free: 0.312 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 

Literature

The X-ray crystal structure of full-length human plasminogen

Law, R.H.P., Caradoc-Davies, T., Cowieson, N., Horvath, A.J., Quek, A.J., Encarnacao, J.A., Steer, D., Cowan, A., Zhang, Q., Lu, B.G.C., Pike, R.N., Smith, A.I., Coughlin, P.B., Whisstock, J.C.

(2012) Cell Rep 1: 185-190

• PubMed: 22832192 
• DOI: 10.1016/j.celrep.2012.02.012
• Primary Citation of Related Structures:  
  4DUR, 4DUU


• PubMed Abstract: 
  

Plasminogen is the proenzyme precursor of the primary fibrinolytic protease plasmin. Circulating plasminogen, which comprises a Pan-apple (PAp) domain, five kringle domains (KR1-5), and a serine protease (SP) domain, adopts a closed, activation-resistant conformation. The kringle domains mediate interactions with fibrin clots and cell-surface receptors. These interactions trigger plasminogen to adopt an open form that can be cleaved and converted to plasmin by tissue-type and urokinase-type plasminogen activators. Here, the structure of closed plasminogen reveals that the PAp and SP domains, together with chloride ions, maintain the closed conformation through interactions with the kringle array. Differences in glycosylation alter the position of KR3, although in all structures the loop cleaved by plasminogen activators is inaccessible. The ligand-binding site of KR1 is exposed and likely governs proenzyme recruitment to targets. Furthermore, analysis of our structure suggests that KR5 peeling away from the PAp domain may initiate plasminogen conformational change.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Plasminogen	A	791	Homo sapiens	Mutation(s): 0  Gene Names: PLG EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens) Explore P00747  Go to UniProtKB:  P00747
PHAROS:  P00747 GTEx:  ENSG00000122194

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.20 Å
• R-Value Free: 0.312 
• R-Value Work: 0.268 
• R-Value Observed: 0.270 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.12	α = 90
b = 110.12	β = 90
c = 234.815	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-22 
• Released Date: 2012-03-28 
Deposition Author(s): Law, R.H.P., Caradoc-Davies, T., Whisstock, J.C.

Revision History  

• Version 1.0: 2012-03-28
  Type: Initial release
  
• Version 1.1: 2012-04-04
  Changes: Structure summary
• Version 1.2: 2013-06-26
  Changes: Database references