5DNF

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin

  • Classification: CYTOKINE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-09-10 Released: 2016-04-13 
  • Deposition Author(s): Liang, W.G., Tang, W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 

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Ligand Structure Quality Assessment 


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Literature

Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3.

Liang, W.G., Triandafillou, C.G., Huang, T.Y., Zulueta, M.M., Banerjee, S., Dinner, A.R., Hung, S.C., Tang, W.J.

(2016) Proc Natl Acad Sci U S A 113: 5000-5005

  • DOI: https://doi.org/10.1073/pnas.1523981113
  • Primary Citation of Related Structures:  
    5CMD, 5COR, 5COY, 5D65, 5DNF

  • PubMed Abstract: 

    • CC chemokine ligand 5 (CCL5) and CCL3 are critical for immune surveillance and inflammation. Consequently, they are linked to the pathogenesis of many inflammatory conditions and are therapeutic targets. Oligomerization and glycosaminoglycan (GAG) binding of CCL5 and CCL3 are vital for the functions of these chemokines ...

    CC chemokine ligand 5 (CCL5) and CCL3 are critical for immune surveillance and inflammation. Consequently, they are linked to the pathogenesis of many inflammatory conditions and are therapeutic targets. Oligomerization and glycosaminoglycan (GAG) binding of CCL5 and CCL3 are vital for the functions of these chemokines. Our structural and biophysical analyses of human CCL5 reveal that CCL5 oligomerization is a polymerization process in which CCL5 forms rod-shaped, double-helical oligomers. This CCL5 structure explains mutational data and offers a unified mechanism for CCL3, CCL4, and CCL5 assembly into high-molecular-weight, polydisperse oligomers. A conserved, positively charged BBXB motif is key for the binding of CC chemokines to GAG. However, this motif is partially buried when CCL3, CCL4, and CCL5 are oligomerized; thus, the mechanism by which GAG binds these chemokine oligomers has been elusive. Our structures of GAG-bound CCL5 and CCL3 oligomers reveal that these chemokine oligomers have distinct GAG-binding mechanisms. The CCL5 oligomer uses another positively charged and fully exposed motif, KKWVR, in GAG binding. However, residues from two partially buried BBXB motifs along with other residues combine to form a GAG-binding groove in the CCL3 oligomer. The N termini of CC chemokines are shown to be involved in receptor binding and oligomerization. We also report an alternative CCL3 oligomer structure that reveals how conformational changes in CCL3 N termini profoundly alter its surface properties and dimer-dimer interactions to affect GAG binding and oligomerization. Such complexity in oligomerization and GAG binding enables intricate, physiologically relevant regulation of CC chemokine functions.

    Organizational Affiliation: 

    Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637; schung@gate.sinica.edu.tw wtang@uchicago.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-C motif chemokine 5
A, B, C, D, E, F, G, H, I
A, B, C, D, E, F, G, H, I
65Homo sapiensMutation(s): 0 
Gene Names: CCL5, D17S136E, SCYA5
UniProt & NIH Common Fund Data Resources
Find proteins for P13501 (Homo sapiens)
Explore P13501 
Go to UniProtKB:  P13501
PHAROS:  P13501
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13501
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoseJ, K, L 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G66470SO
GlyCosmos:  G66470SO
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC
Download Ideal Coordinates CCD File 
DA [auth E],
LA [auth G],
N [auth A],
QA [auth H],
V [auth C]		beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N		 Ligand Interaction
GLA
Query on GLA
Download Ideal Coordinates CCD File 
AA [auth D],
GA [auth F],
M [auth A],
PA [auth H],
U [auth C],
AA [auth D],
GA [auth F],
M [auth A],
PA [auth H],
U [auth C],
UA [auth I]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N		 Ligand Interaction
TRS
Query on TRS
Download Ideal Coordinates CCD File 
T [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
EA [auth E],
HA [auth F],
MA [auth G],
O [auth A],
RA [auth H]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
BA [auth D],
CA [auth D],
FA [auth E],
IA [auth F],
JA [auth F],
BA [auth D],
CA [auth D],
FA [auth E],
IA [auth F],
JA [auth F],
KA [auth F],
NA [auth G],
OA [auth G],
P [auth A],
Q [auth A],
R [auth B],
S [auth B],
SA [auth H],
TA [auth H],
VA [auth I],
W [auth C],
WA [auth I],
X [auth C],
Y [auth C],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.183 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.19α = 90
b = 210.063β = 90
c = 123.827γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2016-05-04
    Changes: Database references
  • Version 1.3: 2016-05-18
    Changes: Database references
  • Version 1.4: 2020-01-15
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary