Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.75 kDa 
• Atom Count: 1842 
• Residue Count: 224 
• Unique protein chains: 2

5BQC

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 and sucrose octasulfate

• DOI: 10.2210/pdb5BQC/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-05-28 Released: 2015-07-01 
• Deposition Author(s): Chang, T.-H., Hsieh, F.-L., Zebisch, M., Harlos, K., Jones, E.Y.
• Funding Organization(s): Medical Research Council (United Kingdom), Cancer Research UK, Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 

Literature

Structure and functional properties of Norrin mimic Wnt for signalling with Frizzled4, Lrp5/6, and proteoglycan.

Chang, T.H., Hsieh, F.L., Zebisch, M., Harlos, K., Elegheert, J., Jones, E.Y.

(2015) Elife 4: e06554

• PubMed: 26158506 
• DOI: 10.7554/eLife.06554
• Primary Citation of Related Structures:  
  5BPB, 5BQC, 5BQB, 5BPU, 5BQ8, 5BPQ, 5BQE


• PubMed Abstract: 
  

Wnt signalling regulates multiple processes including angiogenesis, inflammation, and tumorigenesis. Norrin (Norrie Disease Protein) is a cystine-knot like growth factor. Although unrelated to Wnt, Norrin activates the Wnt/β-catenin pathway. Signal complex formation involves Frizzled4 (Fz4), low-density lipoprotein receptor related protein 5/6 (Lrp5/6), Tetraspanin-12 and glycosaminoglycans (GAGs). Here, we report crystallographic and small-angle X-ray scattering analyses of Norrin in complex with Fz4 cysteine-rich domain (Fz4CRD), of this complex bound with GAG analogues, and of unliganded Norrin and Fz4CRD. Our structural, biophysical and cellular data, map Fz4 and putative Lrp5/6 binding sites to distinct patches on Norrin, and reveal a GAG binding site spanning Norrin and Fz4CRD. These results explain numerous disease-associated mutations. Comparison with the Xenopus Wnt8-mouse Fz8CRD complex reveals Norrin mimics Wnt for Frizzled recognition. The production and characterization of wild-type and mutant Norrins reported here open new avenues for the development of therapeutics to combat abnormal Norrin/Wnt signalling.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-4	B	149	Homo sapiens	Mutation(s): 0  Gene Names: FZD4
Find proteins for Q9ULV1 (Homo sapiens) Explore Q9ULV1  Go to UniProtKB:  Q9ULV1
NIH Common Fund Data Resources
PHAROS:  Q9ULV1 GTEx:  ENSG00000174804

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Norrin	A	122	Homo sapiens	Mutation(s): 0  Gene Names: NDP, EVR2
Find proteins for Q00604 (Homo sapiens) Explore Q00604  Go to UniProtKB:  Q00604
NIH Common Fund Data Resources
PHAROS:  Q00604 GTEx:  ENSG00000124479

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose	C	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900013	C	sucrose octasulfate	Oligosaccharide /  Substrate analog		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.217 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.136	α = 90
b = 119.136	β = 90
c = 119.151	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-28 
• Released Date: 2015-07-01 
Deposition Author(s): Chang, T.-H., Hsieh, F.-L., Zebisch, M., Harlos, K., Jones, E.Y.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	G0900084
Cancer Research UK	United Kingdom	C375/A10976
Wellcome Trust	United Kingdom	090532/Z/09/Z

Revision History 

• Version 1.0: 2015-07-01
  Type: Initial release
  
• Version 1.1: 2015-07-22
  Changes: Database references
• Version 1.2: 2015-07-29
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary