Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.04 kDa 
• Atom Count: 346 
• Modelled Residue Count: 46 
• Deposited Residue Count: 46 
• Unique protein chains: 1

1FFM

THE FIRST EGF-LIKE DOMAIN FROM HUMAN BLOOD COAGULATION FVII (FUCOSYLATED AT SER-60), NMR, MINIMIZED AVERAGE STRUCTURE

• PDB DOI: 10.2210/pdb1FFM/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-02-19 Released: 1999-06-16 
• Deposition Author(s): Kao, Y.-H., Lee, G.F., Wang, Y., Starovasnik, M.A., Kelley, R.F., Spellman, M.W., Lerner, L.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 

Literature

The effect of O-fucosylation on the first EGF-like domain from human blood coagulation factor VII.

Kao, Y.H., Lee, G.F., Wang, Y., Starovasnik, M.A., Kelley, R.F., Spellman, M.W., Lerner, L.

(1999) Biochemistry 38: 7097-7110

• PubMed: 10353820 
• DOI: 10.1021/bi990234z
• Primary Citation of Related Structures:  
  1F7E, 1F7M, 1FF7, 1FFM


• PubMed Abstract: 
  

The first epidermal growth factor-like domain (EGF-1) from blood coagulation factor VII (FVII) contains two unusual O-linked glycosylation sites at Ser-52 and Ser-60. We report here a detailed study of the effect of O-fucosylation at Ser-60 on the structure of FVII EGF-1, its Ca2+-binding affinity, and its interaction with tissue factor (TF). The in vitro fucosylation of the nonglycosylated FVII EGF-1 was achieved by using O-fucosyltransferase purified from Chinese hamster ovary cells. Distance and dihedral constraints derived from NMR data were used to determine the solution structures of both nonglycosylated and fucosylated FVII EGF-1 in the presence of CaCl2. The overall structure of fucosylated FVII EGF-1 is very similar to the nonfucosylated form even for the residues near the fucosylation site. The Ca2+ dissociation constants (Kd) for the nonfucosylated and fucosylated FVII EGF-1 were found to be 16.4 +/- 1.8 and 8.6 +/- 1.4 mM, respectively. The FVII EGF-1 domain binds to the extracellular part of TF with a low affinity (Kd approximately 0. 6 mM), and the addition of fucose appears to have no effect on this affinity. These results indicate that the FVII EGF-1 alone cannot form a tight complex with TF and suggest that the high binding affinity of FVIIa for TF requires cooperative interaction among the four domains in FVII with TF. Although the fucose has no significant effect on the interaction between TF and the individual FVII EGF-1 domain, it may affect the interaction of full-length FVIIa with TF by influencing its Ca2+-binding affinity.

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Organizational Affiliation: 

Department of Analytical Chemistry, Genentech, Inc., South San Francisco, California 94080, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (Blood Coagulation Factor VII)	A	46	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FUC	B [auth A]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 1 
• OLDERADO: 1FFM Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-19 
• Released Date: 1999-06-16 
Deposition Author(s): Kao, Y.-H., Lee, G.F., Wang, Y., Starovasnik, M.A., Kelley, R.F., Spellman, M.W., Lerner, L.

Revision History  

• Version 1.0: 1999-06-16
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary