Macromolecule Content

• Total Structure Weight: 6629.70 
• Atom Count: 466 
• Residue Count: 56 
• Unique protein chains: 1

1EJP

SOLUTION STRUCTURE OF THE SYNDECAN-4 WHOLE CYTOPLASMIC DOMAIN

• DOI: 10.2210/pdb1EJP/pdb
• BMRB: 4591

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens


• Deposited: 2000-03-03 Released: 2001-09-19 
• Deposition Author(s): Lee, D., Oh, E.S., Woods, A., Couchman, J.R., Lee, W.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 90 
• Conformers Submitted: 16 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the dimeric cytoplasmic domain of syndecan-4.

Shin, J., Lee, W., Lee, D., Koo, B.K., Han, I., Lim, Y., Woods, A., Couchman, J.R., Oh, E.S.

(2001) Biochemistry 40: 8471-8478

• PubMed: 11456484 


• PubMed Abstract: 
  

The syndecans, transmembrane proteoglycans which are involved in the organization of cytoskeleton and/or actin microfilaments, have important roles as cell surface receptors during cell-cell and/or cell-matrix interactions. Since previous studies indicate that the function of the syndecan-4 cytoplasmic domain is dependent on its oligomeric status, the conformation of the syndecan-4 cytoplasmic domain itself is important in the understanding of its biological roles. Gel filtration results show that the syndecan-4 cytoplasmic domain (4L) itself forms a dimer stabilized by ionic interactions between peptides at physiological pH. Commensurately, the NMR structures demonstrate that syndecan-4L is a compact intertwined dimer with a symmetric clamp shape in the central variable V region with a root-mean-square deviation between backbone atom coordinates of 0.95 A for residues Leu(186)-Ala(195). The molecular surface of the 4L dimer is highly positively charged. In addition, no intersubunit NOEs in membrane proximal amino acid resides (C1 region) have been observed, demonstrating that the C1 region is mostly unstructured in the syndecan-4L dimer. Interestingly, two parallel strands of 4L form a cavity in the center of the dimeric twist similar to our previously reported 4V structure. The overall topology of the central variable region within the 4L structure is very similar to that of 4V complexed with the phosphatidylinositol 4,5-bisphosphate; however, the intersubunit interaction mode is affected by the presence of C1 and C2 regions. Therefore, we propose that although the 4V region in the full cytoplasmic domain has a tendency for strong peptide--peptide interaction, it may not be enough to overcome the repulsion of the C1 regions of syndecan-4L.

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Organizational Affiliation: 

Department of Biochemistry, College of Science, Yonsei University, Seoul 120-740, Korea.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
SYNDECAN-4	A, B	28	Homo sapiens	Mutation(s): 0  Gene Names: SDC4
Find proteins for P31431 (Homo sapiens) Go to Gene View: SDC4 Go to UniProtKB:  P31431

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 90 
• Conformers Submitted: 16 
• Selection Criteria: structures with the lowest energy 
• Olderado: 1EJP Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-03 
• Released Date: 2001-09-19 
• Deposition Author(s): Lee, D., Oh, E.S., Woods, A., Couchman, J.R., Lee, W.

Revision History 

• Version 1.0: 2001-09-19
  Type: Initial release
• Version 1.1: 2008-04-27
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance