Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 16.28 kDa 
• Atom Count: 1222 
• Modelled Residue Count: 132 
• Deposited Residue Count: 136 
• Unique protein chains: 1

1U4M

human RANTES complexed to heparin-derived disaccharide III-S

• DOI: 10.2210/pdb1U4M/pdb

• Classification: ATTRACTANT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-07-26 Released: 2004-11-09 
• Deposition Author(s): Shaw, J.P., Johnson, Z., Borlat, F., Zwahlen, C., Kungl, A., Roulin, K., Harrenga, A., Wells, T.N.C., Proudfoot, A.E.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.200 

Literature

The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors.

Shaw, J.P., Johnson, Z., Borlat, F., Zwahlen, C., Kungl, A., Roulin, K., Harrenga, A., Wells, T.N., Proudfoot, A.E.

(2004) Structure 12: 2081-2093

• PubMed: 15530372 
• DOI: 10.1016/j.str.2004.08.014
• Primary Citation of Related Structures:  
  1U4M, 1U4L, 1U4R, 1U4P


• PubMed Abstract: 
  

The biological activity of chemokines requires interactions with cell surface proteoglycans. We have determined the structure of the chemokine RANTES (regulated on activation normal T cell expressed) in the presence of heparin-derived disaccharide analogs by X-ray crystallography. These structures confirm the essential role of the BBXB motif in the interaction between the chemokine and the disaccharide. Unexpected interactions were observed in the 30s loop and at the amino terminus. Mutant RANTES molecules were designed to abrogate these interactions and their biological activity examined in vivo. The K45E mutant within the BBXB motif lost the capacity to bind heparin and the ability to elicit cellular recruitment. The Y3A mutant maintained its capacity to bind heparin but was unable to elicit cellular recruitment. Finally, a tetrasaccharide is the smallest oligosaccharide which effectively abolishes the ability of RANTES to recruit cells in vivo. These crystallographic structures provide a description of the molecular interaction of a chemokine with glycosaminoglycans.

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Organizational Affiliation: 

Serono Pharmaceutical Research Institute, 14 Chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Small inducible cytokine A5	A, B	68	Homo sapiens	Mutation(s): 0  Gene Names: CCL5, SCYA5, D17S136E
Find proteins for P13501 (Homo sapiens) Explore P13501  Go to UniProtKB:  P13501
NIH Common Fund Data Resources
PHAROS:  P13501 GTEx:  ENSG00000271503

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose	C	2		N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACY	B	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900094	C	HEPARIN DISACCHARIDE III-S	Oligosaccharide /  Substrate analog		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.252 
• R-Value Work: 0.200 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.074	α = 90
b = 56.415	β = 90
c = 94.354	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-26 
• Released Date: 2004-11-09 
Deposition Author(s): Shaw, J.P., Johnson, Z., Borlat, F., Zwahlen, C., Kungl, A., Roulin, K., Harrenga, A., Wells, T.N.C., Proudfoot, A.E.I.

Revision History  

• Version 1.0: 2004-11-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary