5CL1

Complex structure of Norrin with human Frizzled 4

• PDB DOI: https://doi.org/10.2210/pdb5CL1/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli O157:H7, Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2015-08-12 
• Deposition Author(s): Wang, Z., Ke, J., Shen, G., Cheng, Z., Xu, H.E., Xu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.310 (Depositor), 0.300 (DCC) 
• R-Value Work: 
  0.262 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.264 (Depositor) 

Starting Model: experimental

Literature

Structural basis of the Norrin-Frizzled 4 interaction.

Shen, G., Ke, J., Wang, Z., Cheng, Z., Gu, X., Wei, Y., Melcher, K., Xu, H.E., Xu, W.

(2015) Cell Res 25: 1078-1081

• PubMed: 26227961 
• DOI: https://doi.org/10.1038/cr.2015.92
• Primary Citation of Related Structures:  
  5CL1, 5CM4

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Organizational Affiliation: 

Department of Biological Structure, University of Washington, Seattle, WA 98195, USA.

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 - B2 

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: 138.41 kDa 
• Atom Count: 9,227 
• Modelled Residue Count: 1,177 
• Deposited Residue Count: 1,228 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,Norrin	A, B	483	Escherichia coli O157:H7, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, Z5632, ECs5017, NDP, EVR2
UniProt & NIH Common Fund Data Resources
Find proteins for Q00604 (Homo sapiens) Explore Q00604  Go to UniProtKB:  Q00604
PHAROS:  Q00604 GTEx:  ENSG00000124479
Find proteins for P0AEY0 (Escherichia coli O157:H7) Explore P0AEY0  Go to UniProtKB:  P0AEY0
UniProt Groups	P0AEY0Q00604

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-4	C, D	131	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth C], F [auth C], G [auth D], H [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.310 (Depositor), 0.300 (DCC) 
• R-Value Work:  0.262 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.264 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.291	α = 90
b = 150.589	β = 90
c = 92.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Wang, Z., Ke, J., Shen, G., Cheng, Z., Xu, H.E., Xu, W.

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-16
  Changes: Structure summary