4Z6A

Crystal Structure of a FVIIa-Trypsin Chimera (YT) in Complex with Soluble Tissue Factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity.

Sorensen, A.B.Madsen, J.J.Svensson, L.A.Pedersen, A.A.stergaard, H.Overgaard, M.T.Olsen, O.H.Gandhi, P.S.

(2016) J Biol Chem 291: 4671-4683

  • DOI: 10.1074/jbc.M115.698613
  • Primary Citation of Related Structures:  
    4YLQ, 4Z6A, 4ZMA

  • PubMed Abstract: 
  • The complex of coagulation factor VIIa (FVIIa), a trypsin-like serine protease, and membrane-bound tissue factor (TF) initiates blood coagulation upon vascular injury. Binding of TF to FVIIa promotes allosteric conformational changes in the FVIIa protease domain and improves its catalytic properties ...

    The complex of coagulation factor VIIa (FVIIa), a trypsin-like serine protease, and membrane-bound tissue factor (TF) initiates blood coagulation upon vascular injury. Binding of TF to FVIIa promotes allosteric conformational changes in the FVIIa protease domain and improves its catalytic properties. Extensive studies have revealed two putative pathways for this allosteric communication. Here we provide further details of this allosteric communication by investigating FVIIa loop swap variants containing the 170 loop of trypsin that display TF-independent enhanced activity. Using x-ray crystallography, we show that the introduced 170 loop from trypsin directly interacts with the FVIIa active site, stabilizing segment 215-217 and activation loop 3, leading to enhanced activity. Molecular dynamics simulations and novel fluorescence quenching studies support that segment 215-217 conformation is pivotal to the enhanced activity of the FVIIa variants. We speculate that the allosteric regulation of FVIIa activity by TF binding follows a similar path in conjunction with protease domain N terminus insertion, suggesting a more complete molecular basis of TF-mediated allosteric enhancement of FVIIa activity.


    Organizational Affiliation

    From Global Research, Novo Nordisk A/S, 2760 Måløv, Denmark, pgan@novonordisk.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIA [auth L]96Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIB [auth H]249Homo sapiensMutation(s): 7 
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tissue factorC [auth T]207Homo sapiensMutation(s): 0 
Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
PHAROS:  P13726
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Z6 (Subject of Investigation/LOI)
Query on 0Z6

Download Ideal Coordinates CCD File 
F [auth H]D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-phenylalaninamide
C25 H36 Cl N6 O3
ZKHBINZTIMXMQW-CLAROIROSA-O
 Ligand Interaction
CIT
Query on CIT

Download Ideal Coordinates CCD File 
H [auth T]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
BGC (Subject of Investigation/LOI)
Query on BGC

Download Ideal Coordinates CCD File 
D [auth L]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
FUC (Subject of Investigation/LOI)
Query on FUC

Download Ideal Coordinates CCD File 
E [auth L]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 6
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000369 (0Z6)
Query on PRD_000369
F [auth H]D-Phe-Phe-Arg ChloromethylketonePeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.03α = 90
b = 81.7β = 90
c = 124.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2016-03-09
    Changes: Database references
  • Version 1.3: 2016-12-21
    Changes: Non-polymer description
  • Version 1.4: 2018-01-17
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary