6LCA

Crystal structure of human Dishevelled1 PDZ domain homotrimer

• PDB DOI: https://doi.org/10.2210/pdb6LCA/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-11-18 Released: 2020-11-25 
• Deposition Author(s): Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.273 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 

Starting Model: experimental

Literature

Crystal structure of human Dishevelled1 PDZ domain homotrimer

Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 86.94 kDa 
• Atom Count: 5,430 
• Modelled Residue Count: 722 
• Deposited Residue Count: 816 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Segment polarity protein dishevelled homolog DVL-1	A, B, C, D, E, F, G, H	102	Homo sapiens	Mutation(s): 2  Gene Names: DVL1
UniProt & NIH Common Fund Data Resources
Find proteins for O14640 (Homo sapiens) Explore O14640  Go to UniProtKB:  O14640
PHAROS:  O14640 GTEx:  ENSG00000107404

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.273 
• R-Value Work: 0.245 
• R-Value Observed: 0.246 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.923	α = 90
b = 147.923	β = 90
c = 78.999	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Yasukochi, S., Numoto, N., Tenno, N., Tenno, T., Ito, N., Hiroaki, H.

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description