3LCP | pdb_00003lcp

Crystal structure of the carbohydrate recognition domain of LMAN1 in complex with MCFD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 
    0.247 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.199 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the LMAN1-CRD/MCFD2 transport receptor complex provides insight into combined deficiency of factor V and factor VIII.

Wigren, E.Bourhis, J.M.Kursula, I.Guy, J.E.Lindqvist, Y.

(2010) FEBS Lett 584: 878-882

  • DOI: https://doi.org/10.1016/j.febslet.2010.02.009
  • Primary Citation Related Structures: 
    3LCP

  • PubMed Abstract: 

    LMAN1 is a glycoprotein receptor, mediating transfer from the ER to the ER-Golgi intermediate compartment. Together with the co-receptor MCFD2, it transports coagulation factors V and VIII. Mutations in LMAN1 and MCFD2 can cause combined deficiency of factors V and VIII (F5F8D). We present the crystal structure of the LMAN1/MCFD2 complex and relate it to patient mutations. Circular dichroism data show that the majority of the substitution mutations give rise to a disordered or severely destabilized MCFD2 protein. The few stable mutation variants are found in the binding surface of the complex leading to impaired LMAN1 binding and F5F8D.


  • Organizational Affiliation
    • Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 17177 Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 75.51 kDa 
  • Atom Count: 4,888 
  • Modeled Residue Count: 605 
  • Deposited Residue Count: 680 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein ERGIC-53
A, B
247Homo sapiensMutation(s): 0 
Gene Names: ERGIC53F5F8DLMAN1LMAN1 (AMINO ACIDS 32-277)
UniProt & NIH Common Fund Data Resources
Find proteins for P49257 (Homo sapiens)
Explore P49257 
Go to UniProtKB:  P49257
PHAROS:  P49257
GTEx:  ENSG00000074695 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49257
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Multiple coagulation factor deficiency protein 2
C, D
93Homo sapiensMutation(s): 0 
Gene Names: MCFD2MCFD2 (AMINO ACIDS 58-146)SDNSF
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NI22 (Homo sapiens)
Explore Q8NI22 
Go to UniProtKB:  Q8NI22
PHAROS:  Q8NI22
GTEx:  ENSG00000180398 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NI22
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free:  0.247 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.196 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.602α = 90
b = 58.602β = 90
c = 396.87γ = 120
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-06
    Changes: Structure summary