3A4U

Crystal structure of MCFD2 in complex with carbohydrate recognition domain of ERGIC-53


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency.

Nishio, M.Kamiya, Y.Mizushima, T.Wakatsuki, S.Sasakawa, H.Yamamoto, K.Uchiyama, S.Noda, M.McKay, A.R.Fukui, K.Hauri, H.P.Kato, K.

(2010) Proc Natl Acad Sci U S A 107: 4034-4039

  • DOI: 10.1073/pnas.0908526107
  • Primary Citation of Related Structures:  
    3A4U

  • PubMed Abstract: 
  • Combined deficiency of coagulation factors V and VIII (F5F8D), an autosomal recessive disorder characterized by coordinate reduction in the plasma levels of factor V (FV) and factor VIII (FVIII), is genetically linked to mutations in the transmembrane lectin ERGIC-53 and the soluble calcium-binding protein MCFD2 ...

    Combined deficiency of coagulation factors V and VIII (F5F8D), an autosomal recessive disorder characterized by coordinate reduction in the plasma levels of factor V (FV) and factor VIII (FVIII), is genetically linked to mutations in the transmembrane lectin ERGIC-53 and the soluble calcium-binding protein MCFD2. Growing evidence indicates that these two proteins form a complex recycling between the endoplasmic reticulum (ER) and the ER-Golgi intermediate compartment and thereby function as a cargo receptor in the early secretory pathway of FV and FVIII. For better understanding of the mechanisms underlying the functional coordination of ERGIC-53 and MCFD2, we herein characterize their interaction by x-ray crystallographic analysis in conjunction with NMR and ultracentrifugation analyses. Inspection of the combined data reveals that ERGIC-53-CRD binds MCFD2 through its molecular surface remote from the sugar-binding site, giving rise to a 11 complex in solution. The interaction is independent of sugar-binding of ERGIC-53 and involves most of the missense mutation sites of MCFD2 so far reported in F5F8D. Comparison with the previously reported uncomplexed structure of each protein indicates that MCFD2 but not ERGIC-53-CRD undergoes significant conformational alterations upon complex formation. Our findings provide a structural basis for the cooperative interplay between ERGIC-53 and MCFD2 in capturing FV and FVIII.


    Organizational Affiliation

    Department of Structural Biology and Biomolecular Engineering, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein ERGIC-53 A255Homo sapiensMutation(s): 0 
Gene Names: LMAN1ERGIC53F5F8D
Find proteins for P49257 (Homo sapiens)
Explore P49257 
Go to UniProtKB:  P49257
NIH Common Fund Data Resources
PHAROS:  P49257
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Multiple coagulation factor deficiency protein 2 B143Homo sapiensMutation(s): 0 
Gene Names: MCFD2SDNSF
Find proteins for Q8NI22 (Homo sapiens)
Explore Q8NI22 
Go to UniProtKB:  Q8NI22
NIH Common Fund Data Resources
PHAROS:  Q8NI22
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.188 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.41α = 90
b = 59.41β = 90
c = 198.842γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance