4WYU

Crystal Structure of Scribble PDZ34 tandem in complex with its target peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


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Literature

Interdomain interface-mediated target recognition by the Scribble PDZ34 supramodule.

Ren, J.Feng, L.Bai, Y.Pei, H.Yuan, Z.Feng, W.

(2015) Biochem J 468: 133-144

  • DOI: 10.1042/BJ20141473
  • Primary Citation of Related Structures:  
    4WYT, 4WYU

  • PubMed Abstract: 
  • Tandem-arranged PDZ [PSD-95 (postsynaptic density-95), Dlg (discs large homologue) and ZO-1 (zonula occludens-1)] domains often form structural and functional supramodules with distinct target-binding properties. In the present study, we found that the two PDZ domains within the PDZ34 tandem of Scribble, a cell polarity regulator, tightly pack in a 'front-to-back' mode to form a compact supramodule ...

    Tandem-arranged PDZ [PSD-95 (postsynaptic density-95), Dlg (discs large homologue) and ZO-1 (zonula occludens-1)] domains often form structural and functional supramodules with distinct target-binding properties. In the present study, we found that the two PDZ domains within the PDZ34 tandem of Scribble, a cell polarity regulator, tightly pack in a 'front-to-back' mode to form a compact supramodule. Although PDZ4 contains a distorted αB/βB pocket, the attachment of PDZ4 to PDZ3 generates an unexpected interdomain pocket that is adjacent to and integrates with the canonical αB/βB pocket of PDZ3 to form an expanded target-binding groove. The structure of the PDZ34-target peptide complex further demonstrated that the peptide binds to this expanded target-binding groove with its upstream residues anchoring into the interdomain pocket directly. Mutations of the interdomain pocket and disruptions of the PDZ34 supramodule both interfere with its target-binding capacity. Therefore, the interdomain interface between the PDZ34 supramodule is intrinsically required for its target recognition and determines its target-binding specificity. This interdomain interface-mediated specific recognition may represent a novel mode of target recognition and would broaden the target-binding versatility for PDZ supramodules. The supramodular nature and target recognition mode of the PDZ34 tandem found in the present study would also help to identify the new binding partners of Scribble and thus may direct further research on the PDZ domain-mediated assembly of Scribble polarity complexes.


    Organizational Affiliation

    *National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein scribble homologA,
C [auth B]
212Homo sapiensMutation(s): 0 
Gene Names: SCRIBCRIB1KIAA0147LAP4SCRB1VARTUL
UniProt & NIH Common Fund Data Resources
Find proteins for Q14160 (Homo sapiens)
Explore Q14160 
Go to UniProtKB:  Q14160
PHAROS:  Q14160
GTEx:  ENSG00000180900 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14160
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide SER-TRP-PHE-GLN-THR-ASP-LEUD [auth C],
B [auth D]
7synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.27α = 90
b = 78.43β = 99.51
c = 94.08γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata processing
PHASERphasing
PDB_EXTRACTdata extraction
SCALAdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
China--

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-21
    Type: Initial release