1L6O

XENOPUS DISHEVELLED PDZ DOMAIN

• PDB DOI: https://doi.org/10.2210/pdb1L6O/pdb

• Classification: GENE REGULATION
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-03-11 Released: 2003-06-03 
• Deposition Author(s): Cheyette, B.N.R., Waxman, J.S., Miller, J.R., Takemaru, K.-I., Sheldahl, L.C., Khlebtsova, N., Fox, E.P., Earnest, T., Moon, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.323 
• R-Value Work: 0.277 
• R-Value Observed: 0.279 

Literature

Dapper, a Dishevelled-associated antagonist of beta-catenin and JNK signaling, is required for notochord formation

Cheyette, B.N.R., Waxman, J.S., Miller, J.R., Takemaru, K.-I., Sheldahl, L.C., Khlebtsova, N., Fox, E.P., Earnest, T., Moon, R.T.

(2002) Dev Cell 2: 449-461

• PubMed: 11970895 
• DOI: https://doi.org/10.1016/s1534-5807(02)00140-5
• Primary Citation of Related Structures:  
  1L6O


• PubMed Abstract: 
  

  Dapper was isolated in a screen for proteins interacting with Dishevelled, a key factor in Wnt signaling. Dapper and Dishevelled colocalize intracellularly and form a complex with Axin, GSK-3, CKI, and beta-catenin. Overexpression of Dapper increases Axin and GSK-3 in this complex, resulting in decreased soluble beta-catenin and decreased activation of beta-catenin-responsive genes. Dapper also inhibits activation by Dishevelled of c-Jun N-terminal kinase (JNK), a component of beta-catenin-independent Frizzled signaling. Inhibition of Dapper activates both beta-catenin-responsive genes and an AP1-responsive promoter, demonstrating that Dapper is a general Dishevelled antagonist. Depletion of maternal Dapper RNA from Xenopus embryos results in loss of notochord and head structures, demonstrating that Dapper is required for normal vertebrate development.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Department of Pharmacology and Center for Developmental Biology, University of Washington School of Medicine, Seattle, WA 98195, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A3B1C1D1 

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

Macromolecule Content

• Total Structure Weight: 34.44 kDa 
• Atom Count: 2,328 
• Modelled Residue Count: 304 
• Deposited Residue Count: 309 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-2	A, B, C	95	Xenopus laevis	Mutation(s): 4
UniProt
Find proteins for P51142 (Xenopus laevis) Explore P51142  Go to UniProtKB:  P51142

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dapper 1	D, E, F	8	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.323 
• R-Value Work: 0.277 
• R-Value Observed: 0.279 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.733	α = 90
b = 84.734	β = 90
c = 123.154	γ = 90

Software Package:

Software Name	Purpose
CCDSYS	data collection
HKL-2000	data reduction
SOLVE	phasing
REFMAC	refinement
CCDSYS	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-06-03 
Deposition Author(s): Cheyette, B.N.R., Waxman, J.S., Miller, J.R., Takemaru, K.-I., Sheldahl, L.C., Khlebtsova, N., Fox, E.P., Earnest, T., Moon, R.T.

Revision History  

• Version 1.0: 2003-06-03
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-30
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary