Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.03 kDa 
• Atom Count: 3023 
• Modelled Residue Count: 374 
• Deposited Residue Count: 375 
• Unique protein chains: 2

2KSB

Substance P in isotropic q=0.25 DMPC/CHAPS/GM1 bicelles as a ligand for NK1R

• PDB DOI: 10.2210/pdb2KSB/pdb
• BMRB: 20117

• Classification: NEUROPEPTIDE RECEPTOR/NEUROPEPTIDE
• Organism(s): Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2009-12-31 Released: 2010-11-03 
• Deposition Author(s): Gayen, A., Mukhopadhyay, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 5 
• Selection Criteria: highest binding energy 

Literature

NMR evidence of GM1-induced conformational change of Substance P using isotropic bicelles

Gayen, A., Goswami, S.K., Mukhopadhyay, C.

(2010) Biochim Biophys Acta 

• PubMed: 20937248 
• DOI: 10.1016/j.bbamem.2010.09.023
• Primary Citation of Related Structures:  
  2KS9, 2KSA, 2KSB


• PubMed Abstract: 
  

Substance P (SP) is one of the target neurotransmitters associated with diseases related to chronic inflammation, pain and depression. The selective receptor for SP, NK(1)R is located in the heterogeneous microdomains or caveolae in membrane. Gangliosides, specifically GM1, are markers of these heterogeneous sites. Also, gangliosides are considered as important regulatory elements in cell-cell recognition and cell signaling. In the present work, we describe the conformations of Substance P in the presence of ternary membrane systems containing GM1 at the physiological concentration. SP is mostly unstructured in water, but appears as extended 3(10) helical or turn III in isotropic bicelles, more pronounced in the presence of GM1. NMR results suggest that, in the GM1 containing bicelles, the peptide is more inserted into the membrane with its C-terminus, while N-terminus lies close to the membrane-water interface. The NMR-derived conformation of SP in GM1 bicelles is docked on homology modeled NK(1)R and resulting interactions satisfy reported mutagenesis, fluorescence, photo-affinity labeling and modeling data. The results highlight efficacy of GM1 in membrane in providing structure in an otherwise flexible neurotransmitter Substance P; thus providing indication that it may be useful also for other neurotransmitter peptides/proteins associated with membrane.

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Organizational Affiliation: 

Department of Chemistry, University of Calcutta, 92 APC Road, Kolkata 700009, India.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Substance-P receptor	A	364	Homo sapiens	Mutation(s): 0  Gene Names: TACR1, NK1R, TAC1R Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P25103 (Homo sapiens) Explore P25103  Go to UniProtKB:  P25103
PHAROS:  P25103 GTEx:  ENSG00000115353

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Substance P	B	11	N/A	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P20366 (Homo sapiens) Explore P20366  Go to UniProtKB:  P20366
PHAROS:  P20366 GTEx:  ENSG00000006128

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 5 
• Selection Criteria: highest binding energy 
• OLDERADO: 2KSB Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-31 
• Released Date: 2010-11-03 
Deposition Author(s): Gayen, A., Mukhopadhyay, C.

Revision History  

• Version 1.0: 2010-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-02-26
  Changes: Data collection, Database references, Other