PDBsum entry 4q2o

Protein binding

PDB id: 4q2o

Contents

Protein chains

92 a.a.

89 a.a.

84 a.a.

Waters ×61

PDB id:

4q2o

Name:

Protein binding

Title:

Pdlim4 pdz in complex with a phage-derived peptide

Structure:

Pdz and lim domain protein 4. Chain: a, b, c, d, e, f. Synonym: lim protein ril, reversion-induced lim protein. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: pdlim4, ril. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.10Å R-factor: 0.250 R-free: 0.292

Authors:

B.A.Appleton,C.Wiesmann

Key ref:

A.Ernst et al. (2014). A structural portrait of the PDZ domain family. J Mol Biol, 426, 3509-3519. PubMed id: 25158098 DOI: 10.1016/j.jmb.2014.08.012

Date:

09-Apr-14 Release date: 10-Sep-14

Protein chains

P50479  (PDLI4_HUMAN) -  PDZ and LIM domain protein 4 from Homo sapiens

Seq: 330 a.a.

Struc: 92 a.a.*

Protein chains

P50479  (PDLI4_HUMAN) -  PDZ and LIM domain protein 4 from Homo sapiens

Seq: 330 a.a.

Struc: 89 a.a.*

Protein chain

P50479  (PDLI4_HUMAN) -  PDZ and LIM domain protein 4 from Homo sapiens

Seq: 330 a.a.

Struc: 84 a.a.*

* PDB and UniProt seqs differ at 17 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2014.08.012

J Mol Biol 426:3509-3519 (2014)

PubMed id: 25158098

A structural portrait of the PDZ domain family.

A.Ernst, B.A.Appleton, Y.Ivarsson, Y.Zhang, D.Gfeller, C.Wiesmann, S.S.Sidhu.

ABSTRACT

PDZ (PSD-95/Discs-large/ZO1) domains are interaction modules that typically bind to specific C-terminal sequences of partner proteins and assemble signaling complexes in multicellular organisms. We have analyzed the existing database of PDZ domain structures in the context of a specificity tree based on binding specificities defined by peptide-phage binding selections. We have identified 16 structures of PDZ domains in complex with high-affinity ligands and have elucidated four additional structures to assemble a structural database that covers most of the branches of the PDZ specificity tree. A detailed comparison of the structures reveals features that are responsible for the diverse specificities across the PDZ domain family. Specificity differences can be explained by differences in PDZ residues that are in contact with the peptide ligands, but these contacts involve both side-chain and main-chain interactions. Most PDZ domains bind peptides in a canonical conformation in which the ligand main chain adopts an extended β-strand conformation by interacting in an antiparallel fashion with a PDZ β-strand. However, a subset of PDZ domains bind peptides with a bent main-chain conformation and the specificities of these non-canonical domains could not be explained based on canonical structures. Our analysis provides a structural portrait of the PDZ domain family, which serves as a guide in understanding the structural basis for the diverse specificities across the family.