5IK5

Laminin A2LG45 C-form, G6/7 bound.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Structural basis of laminin binding to the LARGE glycans on dystroglycan.

Briggs, D.C.Yoshida-Moriguchi, T.Zheng, T.Venzke, D.Anderson, M.E.Strazzulli, A.Moracci, M.Yu, L.Hohenester, E.Campbell, K.P.

(2016) Nat Chem Biol 12: 810-814

  • DOI: https://doi.org/10.1038/nchembio.2146
  • Primary Citation of Related Structures:  
    5IK4, 5IK5, 5IK7, 5IK8

  • PubMed Abstract: 

    Dystroglycan is a highly glycosylated extracellular matrix receptor with essential functions in skeletal muscle and the nervous system. Reduced matrix binding by α-dystroglycan (α-DG) due to perturbed glycosylation is a pathological feature of several forms of muscular dystrophy. Like-acetylglucosaminyltransferase (LARGE) synthesizes the matrix-binding heteropolysaccharide [-glucuronic acid-β1,3-xylose-α1,3-]n. Using a dual exoglycosidase digestion, we confirm that this polysaccharide is present on native α-DG from skeletal muscle. The atomic details of matrix binding were revealed by a high-resolution crystal structure of laminin-G-like (LG) domains 4 and 5 (LG4 and LG5) of laminin-α2 bound to a LARGE-synthesized oligosaccharide. A single glucuronic acid-β1,3-xylose disaccharide repeat straddles a Ca(2+) ion in the LG4 domain, with oxygen atoms from both sugars replacing Ca(2+)-bound water molecules. The chelating binding mode accounts for the high affinity of this protein-carbohydrate interaction. These results reveal a previously uncharacterized mechanism of carbohydrate recognition and provide a structural framework for elucidating the mechanisms underlying muscular dystrophy.


  • Organizational Affiliation

    Department of Life Sciences, Imperial College London, London, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Laminin subunit alpha-2393Mus musculusMutation(s): 0 
Gene Names: Lama2
UniProt
Find proteins for Q60675 (Mus musculus)
Explore Q60675 
Go to UniProtKB:  Q60675
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ60675
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q60675-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose
B
2O-Glycosylation
Glycosylation Resources
GlyTouCan:  G00031MO
GlyCosmos:  G00031MO
GlyGen:  G00031MO
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid-(1-3)-alpha-D-xylopyranose-(1-3)-beta-D-glucopyranuronic acid
D
4N/A
Glycosylation Resources
GlyTouCan:  G02540QB
GlyCosmos:  G02540QB
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4MU
Query on 4MU

Download Ideal Coordinates CCD File 
M [auth A]7-hydroxy-4-methyl-2H-chromen-2-one
C10 H8 O3
HSHNITRMYYLLCV-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
K [auth A]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.39α = 90
b = 110.74β = 90
c = 123.9γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom101748/Z/13/Z

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-24
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary