2PKT

Crystal structure of the human CLP-36 (PDLIM1) bound to the C-terminal peptide of human alpha-actinin-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

Starting Model: other
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wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms

Elkins, J.M.Gileadi, C.Shrestha, L.Phillips, C.Wang, J.Muniz, J.R.Doyle, D.A.

(2010) Protein Sci 19: 731-741

  • DOI: https://doi.org/10.1002/pro.349
  • Primary Citation of Related Structures:  
    2PA1, 2PKT, 2PNT, 2Q3G, 2UZC, 2V1W, 2W7R

  • PubMed Abstract: 

    PDZ domains most commonly bind the C-terminus of their protein targets. Typically the C-terminal four residues of the protein target are considered as the binding motif, particularly the C-terminal residue (P0) and third-last residue (P-2) that form the major contacts with the PDZ domain's "binding groove". We solved crystal structures of seven human PDZ domains, including five of the seven PDLIM family members. The structures of GRASP, PDLIM2, PDLIM5, and PDLIM7 show a binding mode with only the C-terminal P0 residue bound in the binding groove. Importantly, in some cases, the P-2 residue formed interactions outside of the binding groove, providing insight into the influence of residues remote from the binding groove on selectivity. In the GRASP structure, we observed both canonical and noncanonical binding in the two molecules present in the asymmetric unit making a direct comparison of these binding modes possible. In addition, structures of the PDZ domains from PDLIM1 and PDLIM4 also presented here allow comparison with canonical binding for the PDLIM PDZ domain family. Although influenced by crystal packing arrangements, the structures nevertheless show that changes in the positions of PDZ domain side-chains and the alpha B helix allow noncanonical binding interactions. These interactions may be indicative of intermediate states between unbound and fully bound PDZ domain and target protein. The noncanonical "perpendicular" binding observed potentially represents the general form of a kinetic intermediate. Comparison with canonical binding suggests that the rearrangement during binding involves both the PDZ domain and its ligand.


  • Organizational Affiliation

    Structural Genomics Consortium, Oxford University, Oxford, OX3 7DQ, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PDZ and LIM domain protein 191Homo sapiensMutation(s): 0 
Gene Names: PDLIM1CLIM1CLP36
UniProt & NIH Common Fund Data Resources
Find proteins for O00151 (Homo sapiens)
Explore O00151 
Go to UniProtKB:  O00151
PHAROS:  O00151
GTEx:  ENSG00000107438 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00151
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
F [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

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G [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACT
Query on ACT

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E [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

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B [auth A],
C [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.74α = 90
b = 38.74β = 90
c = 246.46γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2021-06-23
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-21
    Changes: Advisory, Data collection, Database references
  • Version 1.6: 2024-04-03
    Changes: Refinement description