5Y70 | pdb_00005y70

NMR structure of KMP11 in DPC micelle

• PDB DOI: https://doi.org/10.2210/pdb5Y70/pdb
• BMRB: 36112

• Classification: MEMBRANE PROTEIN
• Organism(s): Trypanosoma brucei brucei
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2017-08-16 Released: 2018-02-07 
• Deposition Author(s): Lu, Y., Lim, L.Z., Song, J.
• Funding Organization(s): Ministry of Education (Singapore)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: target function 

Literature

Kinetoplastid membrane protein-11 adopts a four-helix bundle fold in DPC micelle.

Lim, L.Z., Ee, S., Fu, J., Tan, Y., He, C.Y., Song, J.

(2017) FEBS Lett 591: 3793-3804

• PubMed: 29082514 
• DOI: https://doi.org/10.1002/1873-3468.12891
• Primary Citation Related Structures: 
  5Y70


• PubMed Abstract: 
  

  Kinetoplastid membrane protein-11 (KMP11) is a membrane-associated surface protein of kinetoplastids, which has a strong antigenicity but no mammalian homolog, thus representing a promising vaccine candidate. Here, by CD and NMR, we revealed that in buffer, KMP11 assumes a highly helical conformation without stable tertiary packing. Remarkably, upon interacting with dodecylphosphocholine (DPC) micelle, despite minor changes in secondary structures, KMP11 undergoes rearrangements to form a defined structure. We found that its three-dimensional structure unexpectedly adopts the classic four-helix bundle fold. The surface constituted by the N-/C-termini and conserved loop was characterized to dynamically interact with the polar phase of DPC micelle. Our results provide a structural basis for understanding KMP11 functions and further offer a promising avenue for engineering better vaccines. The structure coordinate of KMP11 in DPC micelle has been deposited in PDB with ID of 5Y70 and the associated NMR data were deposited in BMRB with ID of 36112.

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Organizational Affiliation: 
• Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 12.07 kDa 
• Atom Count: 778 
• Modeled Residue Count: 92 
• Deposited Residue Count: 100 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinetoplastid membrane protein 11	A	100	Trypanosoma brucei brucei	Mutation(s): 0  Gene Names: KMP-11/1, KMP-11/2, KMP-11/3, KMP-11/4
UniProt
Find proteins for P69300 (Trypanosoma brucei brucei) Explore P69300  Go to UniProtKB:  P69300

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 15 
• Selection Criteria: target function 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-07 
Deposition Author(s): Lu, Y., Lim, L.Z., Song, J.

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Funding Organization	Location	Grant Number
Ministry of Education (Singapore)	Singapore	MOE2015 T2 1 111

Revision History  

• Version 1.0: 2018-02-07
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references