Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.22 kDa 
• Atom Count: 4084 
• Modelled Residue Count: 508 
• Deposited Residue Count: 557 
• Unique protein chains: 1

4NZQ

Crystal structure of Ca2+-free prothrombin deletion mutant residues 146-167

• PDB DOI: 10.2210/pdb4NZQ/pdb

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


• Deposited: 2013-12-12 Released: 2014-05-21 
• Deposition Author(s): Pozzi, N., Chen, Z., Shropshire, D.B., Pelc, L.A., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.279 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

The linker connecting the two kringles plays a key role in prothrombin activation.

Pozzi, N., Chen, Z., Pelc, L.A., Shropshire, D.B., Di Cera, E.

(2014) Proc Natl Acad Sci U S A 111: 7630-7635

• PubMed: 24821807 
• DOI: 10.1073/pnas.1403779111
• Primary Citation of Related Structures:  
  4NZQ, 4O03


• PubMed Abstract: 
  

The zymogen prothrombin is proteolytically converted by factor Xa to the active protease thrombin in a reaction that is accelerated >3,000-fold by cofactor Va. This physiologically important effect is paradigmatic of analogous cofactor-dependent reactions in the coagulation and complement cascades, but its structural determinants remain poorly understood. Prothrombin has three linkers connecting the N-terminal Gla domain to kringle-1 (Lnk1), the two kringles (Lnk2), and kringle-2 to the C-terminal protease domain (Lnk3). Recent developments indicate that the linkers, and particularly Lnk2, confer on the zymogen significant flexibility in solution and enable prothrombin to sample alternative conformations. The role of this flexibility in the context of prothrombin activation was tested with several deletions. Removal of Lnk2 in almost its entirety (ProTΔ146-167) drastically reduces the enhancement of thrombin generation by cofactor Va from >3,000-fold to 60-fold because of a significant increase in the rate of activation in the absence of cofactor. Deletion of Lnk2 mimics the action of cofactor Va and offers insights into how prothrombin is activated at the molecular level. The crystal structure of ProTΔ146-167 reveals a contorted architecture where the domains are not vertically stacked, kringle-1 comes within 9 Å of the protease domain, and the Gla-domain primed for membrane binding comes in contact with kringle-2. These findings broaden our molecular understanding of a key reaction of the blood coagulation cascade where cofactor Va enhances activation of prothrombin by factor Xa by compressing Lnk2 and morphing prothrombin into a conformation similar to the structure of ProTΔ146-167.

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Related Citations: 

• Crystal structure of prethrombin-1
  Chen, Z., Pelc, L.A., Di Cera, E.
  (2010) Proc Natl Acad Sci U S A 107: 19278

• Structure of bovine prothrombin fragment 1 refined at 2.25 A resolution
  Seshadri, T.P., Tulinsky, A., Skrzypczak-Jankun, E., Park, C.H.
  (1991) J Mol Biol 220: 481

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Organizational Affiliation: 

Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104 [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	557	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	A	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.81 Å
• R-Value Free: 0.279 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.754	α = 90
b = 171.739	β = 90
c = 141.252	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-12 
• Released Date: 2014-05-21 
Deposition Author(s): Pozzi, N., Chen, Z., Shropshire, D.B., Pelc, L.A., Di Cera, E.

Revision History  

• Version 1.0: 2014-05-21
  Type: Initial release
  
• Version 1.1: 2014-06-25
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary