6ITH | pdb_00006ith

Structure of the transmembrane domain of syndecan 2 in micelles

• PDB DOI: https://doi.org/10.2210/pdb6ITH/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2018-11-23 Released: 2019-02-27 
• Deposition Author(s): Li, Q., Ng, H.Q., Kang, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the least restraint violations 

Literature

Secondary structure and topology of the transmembrane domain of Syndecan-2 in detergent micelles.

Li, Q., Ng, H.Q., Kang, C.

(2019) FEBS Lett 593: 554-561

• PubMed: 30742705 
• DOI: https://doi.org/10.1002/1873-3468.13335
• Primary Citation Related Structures: 
  6ITH


• PubMed Abstract: 
  

  Syndecans are single-span membrane proteins playing important roles in cell-cell and cell-matrix interactions. The transmembrane domain of syndecans is critical for signal transduction across the cell membrane. Here, the structure of the transmembrane domain of syndecan-2 in detergent micelles was investigated using solution NMR spectroscopy. Backbone resonance assignment was obtained, and NMR studies show that the transmembrane domain forms a helix in detergent micelles, which is also supported by the hydrogen and deuterium exchange experiment. A study of the dynamics revealed the rigid structure of the transmembrane domain formed in solution, and paramagnetic relaxation enhancement defined the topology of the transmembrane domain in detergent micelles. This structural analysis may facilitate a better understanding of the role of the syndecan-2 transmembrane domain in signal transduction.

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Organizational Affiliation: 
• Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research (A*STAR), Jurong Island, Singapore.
Experimental Therapeutics Centre, Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.72 kDa 
• Atom Count: 272 
• Modeled Residue Count: 35 
• Deposited Residue Count: 41 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Syndecan-2	A	41	Homo sapiens	Mutation(s): 0  Gene Names: SDC2, HSPG1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P34741 (Homo sapiens) Explore P34741  Go to UniProtKB:  P34741
PHAROS:  P34741 GTEx:  ENSG00000169439

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-27 
Deposition Author(s): Li, Q., Ng, H.Q., Kang, C.

Revision History  

• Version 1.0: 2019-02-27
  Type: Initial release
  
• Version 1.1: 2019-03-27
  Changes: Data collection, Database references
• Version 1.2: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references