5IK7 | pdb_00005ik7

Laminin A2LG45 I-form, Apo.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.219 (Depositor), 0.222 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.6 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 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.

Macromolecule Content 

  • Total Structure Weight: 84.42 kDa 
  • Atom Count: 6,348 
  • Modeled Residue Count: 761 
  • Deposited Residue Count: 762 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Laminin subunit alpha-2
A, B
381Mus 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: 1Go to GlyGen: Q60675-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
G [auth A],
M [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FLC

Query on FLC



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
I [auth A],
L [auth B]
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
EDO

Query on EDO



Download:Ideal Coordinates CCD File
H [auth A],
N [auth B],
O [auth B],
P [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
J [auth B],
K [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.219 (Depositor), 0.222 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.068α = 90
b = 129.083β = 90
c = 147.054γ = 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 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-11-06
    Changes: Structure summary