5BQE

Crystal structure of Norrin in complex with the cysteine-rich domain of Frizzled 4 -Methylated form

• PDB DOI: https://doi.org/10.2210/pdb5BQE/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., 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: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 44.71 kDa 
• Atom Count: 2,711 
• Modelled Residue Count: 324 
• Deposited Residue Count: 393 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Norrin	A	122	Homo sapiens	Mutation(s): 0  Gene Names: NDP, EVR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00604 (Homo sapiens) Explore Q00604  Go to UniProtKB:  Q00604
PHAROS:  Q00604 GTEx:  ENSG00000124479

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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-4	C	149	Homo sapiens	Mutation(s): 0  Gene Names: FZD4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULV1 (Homo sapiens) Explore Q9ULV1  Go to UniProtKB:  Q9ULV1
PHAROS:  Q9ULV1 GTEx:  ENSG00000174804

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG0	D [auth B], E [auth B], H [auth C]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
CL	G [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	B	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.221 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.92	α = 90
b = 98.92	β = 90
c = 120.42	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-07-01 
Deposition Author(s): Chang, T.-H., Hsieh, F.-L., 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 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