5CM4

Crystal structure of human Frizzled 4 Cysteine-Rich Domain (CRD)

• PDB DOI: https://doi.org/10.2210/pdb5CM4/pdb

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


• Deposited: 2015-07-16 Released: 2015-08-12 
• Deposition Author(s): Ke, J., Parker, N., Gu, X., Zhang, C., Melcher, K., Xu, H.E.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.227 (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: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29.38 kDa 
• Atom Count: 1,998 
• Modelled Residue Count: 242 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Frizzled-4	A, B	125	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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q9ULV1-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.255 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.227 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.583	α = 90
b = 111.738	β = 90
c = 75.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-08-12 
Deposition Author(s): Ke, J., Parker, N., Gu, X., Zhang, C., Melcher, K., Xu, H.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK071662
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102545
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM104212
Michigan Economic Development Corporation and the Michigan Technology Tri-Corridor	United States	085P1000817

Revision History  

• Version 1.0: 2015-08-12
  Type: Initial release
  
• Version 1.1: 2015-09-16
  Changes: Database references
• Version 1.2: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary