PDBsum entry 1w9q

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Cell adhesion PDB id
Protein chain
163 a.a. *
Waters ×370
* Residue conservation analysis
PDB id:
Name: Cell adhesion
Title: Crystal structure of the pdz tandem of human syntenin in complex with tnefaf peptide
Structure: Syntenin 1. Chain: a, b. Fragment: pdz tandem, residues 113-273. Synonym: syndecan binding protein 1, melanoma differentiation associated protein-9, mda-9, scaffold protein pbp1, pro-tgf-alpha, cytoplasmic domain-interacting protein 18, tacip18. Engineered: yes. Tnefaf peptide.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: sdcbp or mda9 or sycl. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes
1.70Å     R-factor:   0.176     R-free:   0.224
Authors: J.Grembecka,T.Cierpicki,Y.Devedjiev,D.R.Cooper,Z.S.Derewenda
Key ref:
J.Grembecka et al. (2006). The binding of the PDZ tandem of syntenin to target proteins. Biochemistry, 45, 3674-3683. PubMed id: 16533050 DOI: 10.1021/bi052225y
15-Oct-04     Release date:   22-Mar-06    
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Protein chains
Pfam   ArchSchema ?
O00560  (SDCB1_HUMAN) -  Syntenin-1
298 a.a.
163 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     intracellular signal transduction   3 terms 


DOI no: 10.1021/bi052225y Biochemistry 45:3674-3683 (2006)
PubMed id: 16533050  
The binding of the PDZ tandem of syntenin to target proteins.
J.Grembecka, T.Cierpicki, Y.Devedjiev, U.Derewenda, B.S.Kang, J.H.Bushweller, Z.S.Derewenda.
PDZ domains are among the most abundant protein modules in the known genomes. Their main function is to provide scaffolds for membrane-associated protein complexes by binding to the cytosolic, C-terminal fragments of receptors, channels, and other integral membrane proteins. Here, using both heteronuclear NMR and single crystal X-ray diffraction, we show how peptides with different sequences, including those corresponding to the C-termini of syndecan, neurexin, and ephrin B, can simultaneously bind to both PDZ domains of the scaffolding protein syntenin. The PDZ2 domain binds these peptides in the canonical fashion, and an induced fit mechanism allows for the accommodation of a range of side chains in the P(0) and P(-)(2) positions. However, binding to the PDZ1 domain requires that the target peptide assume a noncanonical conformation. These data help explain how syntenin, and perhaps other PDZ-containing proteins, may preferentially bind to dimeric and clustered targets, and provide a mechanistic explanation for the previously reported cooperative ligand binding by syntenin's two PDZ domains.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20461427 K.Kaufmann, N.Shen, L.Mizoue, and J.Meiler (2011).
A physical model for PDZ-domain/peptide interactions.
  J Mol Model, 17, 315-324.  
20509869 H.J.Lee, and J.J.Zheng (2010).
PDZ domains and their binding partners: structure, specificity, and modification.
  Cell Commun Signal, 8, 8.  
20026484 O.Sakarya, C.Conaco, O.Egecioglu, S.A.Solla, T.H.Oakley, and K.S.Kosik (2010).
Evolutionary expansion and specialization of the PDZ domains.
  Mol Biol Evol, 27, 1058-1069.  
20591147 S.Kalyoncu, O.Keskin, and A.Gursoy (2010).
Interaction prediction and classification of PDZ domains.
  BMC Bioinformatics, 11, 357.  
19915143 A.C.McClelland, S.I.Sheffler-Collins, M.S.Kayser, and M.B.Dalva (2009).
Ephrin-B1 and ephrin-B2 mediate EphB-dependent presynaptic development via syntenin-1.
  Proc Natl Acad Sci U S A, 106, 20487-20492.  
19228696 B.Sulka, H.Lortat-Jacob, R.Terreux, F.Letourneur, and P.Rousselle (2009).
Tyrosine dephosphorylation of the syndecan-1 PDZ binding domain regulates syntenin-1 recruitment.
  J Biol Chem, 284, 10659-10671.  
19654410 J.M.Beekman, L.P.Verhagen, N.Geijsen, and P.J.Coffer (2009).
Regulation of myelopoiesis through syntenin-mediated modulation of IL-5 receptor output.
  Blood, 114, 3917-3927.  
19153575 W.Feng, and M.Zhang (2009).
Organization and dynamics of PDZ-domain-related supramodules in the postsynaptic density.
  Nat Rev Neurosci, 10, 87-99.  
18339805 C.N.Chi, L.Elfström, Y.Shi, T.Snäll, A.Engström, and P.Jemth (2008).
Reassessing a sparse energetic network within a single protein domain.
  Proc Natl Acad Sci U S A, 105, 4679-4684.  
17636570 N.Kamiya, Y.Yonezawa, H.Nakamura, and J.Higo (2008).
Protein-inhibitor flexible docking by a multicanonical sampling: native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others.
  Proteins, 70, 41-53.  
17384233 J.M.Elkins, E.Papagrigoriou, G.Berridge, X.Yang, C.Phillips, C.Gileadi, P.Savitsky, and D.A.Doyle (2007).
Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
  Protein Sci, 16, 683-694.
PDB codes: 2byg 2fcf 2fne 2gzv 2he2 2he4 2i1n 2iwn 2iwo 2iwp 2iwq
17279591 M.Paduch, M.Biernat, P.Stefanowicz, Z.S.Derewenda, Z.Szewczuk, and J.Otlewski (2007).
Bivalent peptides as models for multimeric targets of PDZ domains.
  Chembiochem, 8, 443-452.  
17935616 M.Wang, F.D.Guerrero, G.Pertea, and V.M.Nene (2007).
Global comparative analysis of ESTs from the southern cattle tick, Rhipicephalus (Boophilus) microplus.
  BMC Genomics, 8, 368.  
17551586 O.Sakarya, K.A.Armstrong, M.Adamska, M.Adamski, I.F.Wang, B.Tidor, B.M.Degnan, T.H.Oakley, and K.S.Kosik (2007).
A post-synaptic scaffold at the origin of the animal kingdom.
  PLoS ONE, 2, e506.  
17267502 Y.Zhang, J.Dasgupta, R.Z.Ma, L.Banks, M.Thomas, and X.S.Chen (2007).
Structures of a human papillomavirus (HPV) E6 polypeptide bound to MAGUK proteins: mechanisms of targeting tumor suppressors by a high-risk HPV oncoprotein.
  J Virol, 81, 3618-3626.
PDB codes: 2i04 2i0i 2i0l
16908530 N.Latysheva, G.Muratov, S.Rajesh, M.Padgett, N.A.Hotchin, M.Overduin, and F.Berditchevski (2006).
Syntenin-1 is a new component of tetraspanin-enriched microdomains: mechanisms and consequences of the interaction of syntenin-1 with CD63.
  Mol Cell Biol, 26, 7707-7718.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.