4G69 | pdb_00004g69

Structure of the Human Discs Large 1 PDZ2 - Adenomatous Polyposis Coli Cytoskeletal Polarity Complex

• PDB DOI: https://doi.org/10.2210/pdb4G69/pdb

• Classification: MEMBRANE PROTEIN/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-07-18 Released: 2012-12-12 
• Deposition Author(s): Slep, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.183 (Depositor), 0.186 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.169 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structure of the Human Discs Large 1 PDZ2- Adenomatous Polyposis Coli Cytoskeletal Polarity Complex: Insight into Peptide Engagement and PDZ Clustering.

Slep, K.C.

(2012) PLoS One 7: e50097-e50097

• PubMed: 23185543 
• DOI: https://doi.org/10.1371/journal.pone.0050097
• Primary Citation Related Structures: 
  4G69


• PubMed Abstract: 
  

  The membrane associated guanylate kinase (MAGUK) family member, human Discs Large 1 (hDlg1) uses a PDZ domain array to interact with the polarity determinant, the Adenomatous Polyposis Coli (APC) microtubule plus end binding protein. The hDLG1-APC complex mediates a dynamic attachment between microtubule plus ends and polarized cortical determinants in epithelial cells, stem cells, and neuronal synapses. Using its multi-domain architecture, hDlg1 both scaffolds and regulates the polarity factors it engages. Molecular details underlying the hDlg1-APC interaction and insight into how the hDlg1 PDZ array may cluster and regulate its binding factors remain to be determined. Here, I present the crystal structure of the hDlg1 PDZ2-APC complex and the molecular determinants that mediate APC binding. The hDlg1 PDZ2-APC complex also provides insight into potential modes of ligand-dependent PDZ domain clustering that may parallel Dlg scaffold regulatory mechanisms. The hDlg1 PDZ2-APC complex presented here represents a core biological complex that bridges polarized cortical determinants with the dynamic microtubule cytoskeleton.

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Organizational Affiliation: 
• Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 11.81 kDa 
• Atom Count: 875 
• Modeled Residue Count: 103 
• Deposited Residue Count: 111 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Disks large homolog 1	A	100	Homo sapiens	Mutation(s): 0  Gene Names: DLG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q12959 (Homo sapiens) Explore Q12959  Go to UniProtKB:  Q12959
PHAROS:  Q12959 GTEx:  ENSG00000075711

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenomatous polyposis coli protein	B	11	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25054 (Homo sapiens) Explore P25054  Go to UniProtKB:  P25054
PHAROS:  P25054 GTEx:  ENSG00000134982

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.183 (Depositor), 0.186 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.169 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.109	α = 90
b = 51.184	β = 90
c = 71.756	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-12 
Deposition Author(s): Slep, K.C.

Revision History  

• Version 1.0: 2012-12-12
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Refinement description