5EDM | pdb_00005edm

Crystal structure of prothrombin deletion mutant residues 154-167 ( Form I )

• PDB DOI: https://doi.org/10.2210/pdb5EDM/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Mesocricetus auratus
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2015-10-21 Released: 2016-01-20 
• Deposition Author(s): Pozzi, N., Chen, Z., Di Cera, E.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

How the Linker Connecting the Two Kringles Influences Activation and Conformational Plasticity of Prothrombin.

Pozzi, N., Chen, Z., Di Cera, E.

(2016) J Biological Chem 291: 6071-6082

• PubMed: 26763231 
• DOI: https://doi.org/10.1074/jbc.M115.700401
• Primary Citation Related Structures: 
  5EDK, 5EDM


• PubMed Abstract: 
  

  A flexible linker (Lnk2) composed of 26 amino acids connects kringle-1 to kringle-2 in the coagulation factor prothrombin. Recent studies point to Lnk2 as a key determinant of the structure and function of this zymogen. Using a combination of mutagenesis, structural biology, and single molecule spectroscopy, we show how Lnk2 influences activation and conformational plasticity of prothrombin. Scrambling the sequence of Lnk2 is inconsequential on activation, and so is extension by as many as 22 residues. On the other hand, below a critical length of 15 residues, the rate of prothrombin activation increases (10-fold) in the absence of cofactor Va and decreases (3-fold) in the presence of cofactor. Furthermore, activation by prothrombinase takes place without preference along the prethrombin-2 (cleavage at Arg(271) first) or meizothrombin (cleavage at Arg(320) first) pathways. Notably, these transitions in the rate and pathway of activation require the presence of phospholipids, pointing to an important physiological role for Lnk2 when prothrombin is anchored to the membrane. Two new crystal structures of prothrombin lacking 22 (ProTΔ146-167) or 14 (ProTΔ154-167) residues of Lnk2 document striking conformational rearrangements of domains located across this linker. FRET measurements of freely diffusing single molecules prove that these structural transitions are genuine properties of the zymogen in solution. These findings support a molecular model of prothrombin activation where Lnk2 presents the sites of cleavage at Arg(271) and Arg(320) to factor Xa in different orientations by pivoting the C-terminal kringle-2/protease domain pair on the N-terminal Gla domain/kringle-1 pair anchored to the membrane.

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Organizational Affiliation: 
• From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104.
From the Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, Missouri 63104 [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 67.01 kDa 
• Atom Count: 5,005 
• Modeled Residue Count: 550 
• Deposited Residue Count: 568 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A	568	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P00734-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], T [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	S [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-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: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.884	α = 90
b = 168.69	β = 90
c = 144.315	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Pozzi, N., Chen, Z., Di Cera, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	HL049413, HL073813 and HL112303 (EDC)

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2016-03-30
  Changes: Database references
• Version 1.3: 2017-08-09
  Changes: Database references, Derived calculations
• Version 1.4: 2017-09-06
  Changes: Author supporting evidence
• Version 1.5: 2019-12-04
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2023-11-15
  Changes: Data collection