1N99

CRYSTAL STRUCTURE OF THE PDZ TANDEM OF HUMAN SYNTENIN

• PDB DOI: https://doi.org/10.2210/pdb1N99/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2002-11-22 Released: 2003-04-15 
• Deposition Author(s): Kang, B.S., Cooper, D.R., Jelen, F., Devedjiev, Y., Derewenda, U., Dauter, Z., Otlewski, J., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.227 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

PDZ Tandem of Human Syntenin: Crystal Structure and Functional Properties

Kang, B.S., Cooper, D.R., Jelen, F., Devedjiev, Y., Derewenda, U., Dauter, Z., Otlewski, J., Derewenda, Z.S.

(2003) Structure 11: 459-468

• PubMed: 12679023 
• DOI: https://doi.org/10.1016/s0969-2126(03)00052-2
• Primary Citation of Related Structures:  
  1N99


• PubMed Abstract: 
  

  Syntenin, a 33 kDa protein, interacts with several cell membrane receptors and with merlin, the product of the causal gene for neurofibromatosis type II. We report a crystal structure of the functional fragment of human syntenin containing two canonical PDZ domains, as well as binding studies for full-length syntenin, the PDZ tandem, and isolated PDZ domains. We show that the functional properties of syntenin are a result of independent interactions with target peptides, and that each domain is able to bind peptides belonging to two different classes: PDZ1 binds peptides from classes I and III, while PDZ2 interacts with classes I and II. The independent binding of merlin by PDZ1 and syndecan-4 by PDZ2 provides direct evidence for the coupling of syndecan-mediated signaling to actin regulation by merlin.

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Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics and The Cancer Center, University of Virginia, Charlottesville, VA 22908, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.41 kDa 
• Atom Count: 2,708 
• Modelled Residue Count: 325 
• Deposited Residue Count: 332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syntenin 1	A, B	166	Homo sapiens	Mutation(s): 3  Gene Names: SDCBP OR MDA9 OR SYCL
UniProt & NIH Common Fund Data Resources
Find proteins for O00560 (Homo sapiens) Explore O00560  Go to UniProtKB:  O00560
PHAROS:  O00560 GTEx:  ENSG00000137575

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.227 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.727	α = 90
b = 48.678	β = 120.82
c = 74.69	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
TRUNCATE	data reduction
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-04-15 
Deposition Author(s): Kang, B.S., Cooper, D.R., Jelen, F., Devedjiev, Y., Derewenda, U., Dauter, Z., Otlewski, J., Derewenda, Z.S.

Revision History  

• Version 1.0: 2003-04-15
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2022-12-21
  Changes: Database references, Derived calculations
• Version 1.4: 2024-11-06
  Changes: Data collection, Structure summary