Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

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

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.35 kDa 
• Atom Count: 2796 
• Modelled Residue Count: 315 
• Deposited Residue Count: 323 
• Unique protein chains: 2

1KLI

Cofactor-and substrate-assisted activation of factor VIIa

• PDB DOI: 10.2210/pdb1KLI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2001-12-12 Released: 2002-09-18 
• Deposition Author(s): Sichler, K., Banner, D.W., D'Arcy, A., Hopfner, K.P., Huber, R., Bode, W., Kresse, G.B., Kopetzki, E., Brandstetter, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Literature

Crystal Structure of Uninhibited Factor VIIa Link its Cofactor and Substrate-assisted Activation to Specific Interactions

Sichler, K., Banner, D.W., D'Arcy, A., Hopfner, K.P., Huber, R., Bode, W., Kresse, G.B., Kopetzki, E., Brandstetter, H.

(2002) J Mol Biol 322: 591-603

• PubMed: 12225752 
• DOI: 10.1016/s0022-2836(02)00747-7
• Primary Citation of Related Structures:  
  1KLI, 1KLJ


• PubMed Abstract: 
  

Factor VIIa initiates the extrinsic coagulation cascade; this event requires a delicately balanced regulation that is implemented on different levels, including a sophisticated multi-step activation mechanism of factor VII. Its central role in hemostasis and thrombosis makes factor VIIa a key target of pharmaceutical research. We succeeded, for the first time, in recombinantly producing N-terminally truncated factor VII (rf7) in an Escherichia coli expression system by employing an oxidative, in vitro, folding protocol, which depends critically on the presence of ethylene glycol. Activated recombinant factor VIIa (rf7a) was crystallised in the presence of the reversible S1-site inhibitor benzamidine. Comparison of this 1.69A crystal structure with that of an inhibitor-free and sulphate-free, but isomorphous crystal form identified structural details of factor VIIa stimulation. The stabilisation of Asp189-Ser190 by benzamidine and the capping of the intermediate helix by a sulphate ion appear to be sufficient to mimic the disorder-order transition conferred by the cofactor tissue factor (TF) and the substrate factor X. Factor VIIa shares with the homologous factor IXa, but not factor Xa, a bell-shaped activity modulation dependent on ethylene glycol. The ethylene glycol-binding site of rf7a was identified in the vicinity of the 60 loop. Ethylene glycol binding induces a significant conformational rearrangement of the 60 loop. This region serves as a recognition site of the physiologic substrate, factor X, which is common to both factor VIIa and factor IXa. These results provide a mechanistic framework of substrate-assisted catalysis of both factor VIIa and factor IXa.

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Organizational Affiliation: 

Max-Planck-Institut für Biochemie, D-82152, Martinsried, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
factor VIIa	A [auth L]	69	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
factor VIIa	B [auth H]	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
PHAROS:  P08709 GTEx:  ENSG00000057593

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEN	H	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
SO4	C [auth H], D [auth H], E [auth H], F [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	G [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.225 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.443	α = 90
b = 94.443	β = 90
c = 114.315	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-12-12 
• Released Date: 2002-09-18 
Deposition Author(s): Sichler, K., Banner, D.W., D'Arcy, A., Hopfner, K.P., Huber, R., Bode, W., Kresse, G.B., Kopetzki, E., Brandstetter, H.

Revision History  

• Version 1.0: 2002-09-18
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance