1BF9

N-TERMINAL EGF-LIKE DOMAIN FROM HUMAN FACTOR VII, NMR, 23 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 23 
  • Selection Criteria: NO DISTANCE RESTRAINT VIOLATED BY MORE THAN 0.2 ANGSTROM AND NO DIHEDRAL ANGLE RESTRAINTS VIOLATED BY MORE THAN 2 DEGREES 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Solution structure of the N-terminal EGF-like domain from human factor VII.

Muranyi, A.Finn, B.E.Gippert, G.P.Forsen, S.Stenflo, J.Drakenberg, T.

(1998) Biochemistry 37: 10605-10615

  • DOI: 10.1021/bi980522f

  • PubMed Abstract: 
  • Blood coagulation is initiated by Ca(2+)-dependent binding of coagulation factor VIIa (FVIIa) to its cofactor, tissue factor (TF). The TF:FVIIa complex activates factors IX and X, ultimately leading to the formation of thrombin and the coagulation of ...

    Blood coagulation is initiated by Ca(2+)-dependent binding of coagulation factor VIIa (FVIIa) to its cofactor, tissue factor (TF). The TF:FVIIa complex activates factors IX and X, ultimately leading to the formation of thrombin and the coagulation of blood. FVII consists of an N-terminal gamma-carboxyglutamic-acid-containing (Gla) domain followed by two epidermal growth factor (EGF) like domains, the first of which can bind one Ca2+ ion (Kd approximately 150 microM) and a C-terminal serine protease domain. Using 1H nuclear magnetic resonance spectroscopy, we have determined the solution structure of a synthetic N-terminal EGF-like domain (EGF1) of human FVII (residues 45-85) in the absence of Ca2+. A comparison of this structure of apo EGF1 with the Ca(2+)-bound EGF1 in the complex of FVIIa and TF [Banner, D. W., et al. (1996) Nature 380, 41-46] suggests that the structural changes in the EGF1 domain upon Ca2+ binding are minor and are concentrated near the Ca(2+)-binding site, which is facing away from the TF interaction surface. Amino acid side chains that are crucial for the binding of FVII to TF show a similar conformation in both structures and are therefore unlikely to directly influence the Ca(2+)-dependent binding of FVII to TF. As Ca2+ binding to EGF1 does not lead to a conformational change in the residues constituting the interaction surface for binding to TF, our results are consistent with the idea that the altered orientation between the Gla and EGF1 domains that result from Ca2+ binding is responsible for the increased affinity of FVII/FVIIa for TF.


    Related Citations: 
    • The Three-Dimensional Structure of the First Egf-Like Module of Human Factor Ix: Comparison with Egf and Tgf-Alpha
      Baron, M.,Norman, D.G.,Harvey, T.S.,Handford, P.A.,Mayhew, M.,Tse, A.G.,Brownlee, G.G.,Campbell, I.D.
      (1992) Protein Sci. 1: 81
    • Three-Dimensional Structure of the Apo Form of the N-Terminal Egf-Like Module of Blood Coagulation Factor X as Determined by NMR Spectroscopy and Simulated Folding
      Ullner, M.,Selander, M.,Persson, E.,Stenflo, J.,Drakenberg, T.,Teleman, O.
      (1992) Biochemistry 31: 5974
    • The Crystal Structure of the Complex of Blood Coagulation Factor Viia with Soluble Tissue Factor
      Banner, D.W.,D'Arcy, A.,Chene, C.,Winkler, F.K.,Guha, A.,Konigsberg, W.H.,Nemerson, Y.,Kirchhofer, D.
      (1996) Nature 380: 41


    Organizational Affiliation

    Physical Chemistry 2, Lund University, Sweden. andreas.muranyi@fkem2.lth.se




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACTOR VII
A
41Homo sapiensGene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 23 
  • Selection Criteria: NO DISTANCE RESTRAINT VIOLATED BY MORE THAN 0.2 ANGSTROM AND NO DIHEDRAL ANGLE RESTRAINTS VIOLATED BY MORE THAN 2 DEGREES 
  • Olderado: 1BF9 Olderado
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other