Crystal structure of a carbohydrate-binding domain

Experimental Data Snapshot

  • Resolution: 2.42 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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This is version 1.3 of the entry. See complete history


Structural Characterization of Carbohydrate Binding by LMAN1 Protein Provides New Insight into the Endoplasmic Reticulum Export of Factors V (FV) and VIII (FVIII).

Zheng, C.Page, R.C.Das, V.Nix, J.C.Wigren, E.Misra, S.Zhang, B.

(2013) J Biol Chem 288: 20499-20509

  • DOI: https://doi.org/10.1074/jbc.M113.461434
  • Primary Citation of Related Structures:  
    4GKX, 4GKY

  • PubMed Abstract: 

    LMAN1 (ERGIC-53) is a key mammalian cargo receptor responsible for the export of a subset of glycoproteins from the endoplasmic reticulum. Together with its soluble coreceptor MCFD2, LMAN1 transports coagulation factors V (FV) and VIII (FVIII). Mutations in LMAN1 or MCFD2 cause the genetic bleeding disorder combined deficiency of FV and FVIII (F5F8D). The LMAN1 carbohydrate recognition domain (CRD) binds to both glycoprotein cargo and MCFD2 in a Ca(2+)-dependent manner. To understand the biochemical basis and regulation of LMAN1 binding to glycoprotein cargo, we solved crystal structures of the LMAN1-CRD bound to Man-α-1,2-Man, the terminal carbohydrate moiety of high mannose glycans. Our structural data, combined with mutagenesis and in vitro binding assays, define the central mannose-binding site on LMAN1 and pinpoint histidine 178 and glycines 251/252 as critical residues for FV/FVIII binding. We also show that mannobiose binding is relatively independent of pH in the range relevant for endoplasmic reticulum-to-Golgi traffic, but is sensitive to lowered Ca(2+) concentrations. The distinct LMAN1/MCFD2 interaction is maintained at these lowered Ca(2+) concentrations. Our results suggest that compartmental changes in Ca(2+) concentration regulate glycoprotein cargo binding and release from the LMAN1·MCFD2 complex in the early secretory pathway.

  • Organizational Affiliation

    Genomic Medicine Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein ERGIC-53261Homo sapiensMutation(s): 0 
Gene Names: ERGIC53F5F8DLMAN1
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
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.42 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.263α = 90
b = 110.263β = 90
c = 38.332γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
XDSdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-05
    Type: Initial release
  • Version 1.1: 2013-07-31
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary