5EW6

Structure of ligand binding region of uPARAP at pH 7.4 without calcium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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This is version 2.0 of the entry. See complete history


Literature

Crystal structures of the ligand-binding region of uPARAP: effect of calcium ion binding

Yuan, C.Jurgensen, H.J.Engelholm, L.H.Li, R.Liu, M.Jiang, L.Luo, Z.Behrendt, N.Huang, M.

(2016) Biochem J 473: 2359-2368

  • DOI: 10.1042/BCJ20160276
  • Primary Citation of Related Structures:  
    5E4K, 5EW6

  • PubMed Abstract: 
  • The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR) ...

    The proteins of the mannose receptor (MR) family share a common domain organization and have a broad range of biological functions. Urokinase plasminogen activator receptor-associated protein (uPARAP) (or Endo180) is a member of this family and plays an important role in extracellular matrix remodelling through interaction with its ligands, including collagens and urokinase plasminogen activator receptor (uPAR). We report the crystal structures of the first four domains of uPARAP (also named the ligand-binding region, LBR) at pH 7.4 in Ca(2+)-bound and Ca(2+)-free forms. The first domain (cysteine-rich or CysR domain) folds into a new and unique conformation different from the β-trefoil fold of typical CysR domains. The so-called long loop regions (LLRs) of the C-type lectin-like domain (CTLD) 1 and 2 (the third and fourth domain) mediate the direct contacts between these domains. These LLRs undergo a Ca(2+)-dependent conformational change, and this is likely to be the key structural determinant affecting the overall conformation of uPARAP. Our results provide a molecular mechanism to support the structural flexibility of uPARAP, and shed light on the structural flexibility of other members of the MR family.


    Organizational Affiliation

    State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, China College of Chemistry and Chemical Engineering, Fuzhou University, Fuzhou 350108, China mhuang@fjirsm.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-type mannose receptor 2A492Homo sapiensMutation(s): 1 
Gene Names: MRC2CLEC13EENDO180KIAA0709UPARAP
Find proteins for Q9UBG0 (Homo sapiens)
Explore Q9UBG0 
Go to UniProtKB:  Q9UBG0
NIH Common Fund Data Resources
PHAROS:  Q9UBG0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseB3 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
F [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900017
Query on PRD_900017
Btriacetyl-beta-chitotrioseOligosaccharide /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.11α = 90
b = 78.11β = 90
c = 252.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
xia2data reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-11-20 
  • Released Date: 2016-08-10 
  • Deposition Author(s): Yuan, C., Huang, M.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570745
National Natural Science Foundation of ChinaChina31170707
National Natural Science Foundation of ChinaChina31370737

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary