6LOG

Crystal structure of human CCL5-12AAA14 mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report



Literature

N-terminal Backbone Pairing Shifts in CCL5-12AAA14Dimer Interface: Structural Significance of the FAY Sequence.

Li, J.Y.Chen, Y.C.Lee, Y.Z.Huang, C.H.Sue, S.C.

(2020) Int J Mol Sci 21

  • DOI: 10.3390/ijms21051689
  • Primary Citation of Related Structures:  
    6LOG

  • PubMed Abstract: 
  • CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. ...

    CC-type chemokine ligand 5 (CCL5) has been known to regulate immune responses by mediating the chemotaxis of leukocytes. Depending on the environment, CCL5 forms different orders of oligomers to interact with targets and create functional diversity. A recent CCL5 trimer structure revealed that the N-terminal conversed F12-A13-Y14 ( 12 FAY 14 ) sequence is involved in CCL5 aggregation. The CCL5- 12 AAA 14 mutant with two mutations had a deficiency in the formation of high-order oligomers. In the study, we clarify the respective roles of F12 and Y14 through NMR analysis and structural determination of the CCL5- 12 AAA 14 mutant where F12 is involved in the dimer assembly and Y14 is involved in aggregation. The CCL5- 12 AAA 14 structure contains a unique dimer packing. The backbone pairing shifts for one-residue in the N-terminal interface, when compared to the native CCL5 dimer. This difference creates a new structural orientation and leads to the conclusion that F12 confines the native CCL5 dimer configuration. Without F12 anchoring in the position, the interfacial backbone pairing is permitted to slide. Structural plasticity occurs in the N-terminal interaction. This is the first case to report this structural rearrangement through mutagenesis. The study provides a new idea for chemokine engineering and complements the understanding of CCL5 oligomerization and the role of the 12 FAY 14 sequence.


    Organizational Affiliation

    Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-C motif chemokine 5A69Homo sapiensMutation(s): 2 
Gene Names: CCL5D17S136ESCYA5
Find proteins for P13501 (Homo sapiens)
Explore P13501 
Go to UniProtKB:  P13501
NIH Common Fund Data Resources
PHAROS  P13501
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.329α = 90
b = 48.329β = 90
c = 60.401γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, Taiwan)Taiwan108-2113-M-007-003

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release