1U4M | pdb_00001u4m
human RANTES complexed to heparin-derived disaccharide III-S
- PDB DOI: https://doi.org/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.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.252 (Depositor)
- R-Value Work: 0.200 (Depositor)
Starting Model: experimental
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wwPDB Validation3D Report Full Report
Literature
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Download Mendeley
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 Search on PubMed
- DOI: https://doi.org/10.1016/j.str.2004.08.014
- Primary Citation Related Structures:
1U4L, 1U4M, 1U4P, 1U4R - 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.
- Serono Pharmaceutical Research Institute, 14 Chemin des Aulx, 1228 Plan-les-Ouates, Geneva, Switzerland. jeffrey.shaw@serono.com
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (ACY)
Biological Assembly 1
Explore in 3D: Structure | Sequence Annotations | Validation Report | Ligand Interaction (ACY)
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 16.28 kDa
- Atom Count: 1,222
- Modeled Residue Count: 132
- Deposited Residue Count: 136
- Unique protein chains: 1
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Small inducible cytokine A5 | 68 | Homo sapiens | Mutation(s): 0 Gene Names: CCL5, SCYA5 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
PHAROS: P13501 GTEx: ENSG00000271503 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P13501 | ||||
Sequence AnnotationsExpand | |||||
Reference Sequence | |||||
Oligosaccharides
HelpSmall Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ACY Download:Ideal Coordinates CCD File | D [auth B] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N | 👁 Image | ||
Biologically Interesting Molecules (External Reference)
1 UniqueExperimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.252 (Depositor)
- R-Value Work: 0.200 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 24.074 | α = 90 |
| b = 56.415 | β = 90 |
| c = 94.354 | γ = 90 |
| Software Name | Purpose |
|---|---|
| CNX | refinement |
| DENZO | data reduction |
| SCALEPACK | data scaling |
| AMoRE | phasing |
Entry History
Deposition Data
- 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 (Full details and data files)
- 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 - Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary - Version 2.2: 2024-11-13
Changes: Structure summary
