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2X69 | pdb_00002x69
X-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer
- PDB DOI: https://doi.org/10.2210/pdb2X69/pdb
- Classification: IMMUNE SYSTEM
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2010-02-15 Released: 2010-11-03
- Deposition Author(s): Guo, Q., Ren, M., Tang, W.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.265 (Depositor), 0.265 (DCC)
- R-Value Work: 0.223 (Depositor), 0.230 (DCC)
- R-Value Observed: 0.235 (Depositor)
wwPDB Validation 3D Report Full Report
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Polymerization of Mip-1 Chemokine (Ccl3 and Ccl4) and Clearance of Mip-1 by Insulin-Degrading Enzyme.
Ren, M., Guo, Q., Guo, L., Lenz, M., Qian, F., Koenen, R.R., Xu, H., Schilling, A.B., Weber, C., Ye, R.D., Dinner, A.R., Tang, W.(2010) EMBO J 29: 3952
- PubMed: 20959807 Search on PubMedSearch on PubMed Central
- DOI: https://doi.org/10.1038/emboj.2010.256
- Primary Citation Related Structures:
2X69, 2X6G, 2X6L - PubMed Abstract:
Macrophage inflammatory protein-1 (MIP-1), MIP-1α (CCL3) and MIP-1β (CCL4) are chemokines crucial for immune responses towards infection and inflammation. Both MIP-1α and MIP-1β form high-molecular-weight aggregates. Our crystal structures reveal that MIP-1 aggregation is a polymerization process and human MIP-1α and MIP-1β form rod-shaped, double-helical polymers. Biophysical analyses and mathematical modelling show that MIP-1 reversibly forms a polydisperse distribution of rod-shaped polymers in solution. Polymerization buries receptor-binding sites of MIP-1α, thus depolymerization mutations enhance MIP-1α to arrest monocytes onto activated human endothelium. However, same depolymerization mutations render MIP-1α ineffective in mouse peritoneal cell recruitment. Mathematical modelling reveals that, for a long-range chemotaxis of MIP-1, polymerization could protect MIP-1 from proteases that selectively degrade monomeric MIP-1. Insulin-degrading enzyme (IDE) is identified as such a protease and decreased expression of IDE leads to elevated MIP-1 levels in microglial cells. Our structural and proteomic studies offer a molecular basis for selective degradation of MIP-1. The regulated MIP-1 polymerization and selective inactivation of MIP-1 monomers by IDE could aid in controlling the MIP-1 chemotactic gradient for immune surveillance.
- Ben-May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 1 generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 2 generated by PISA (software)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report
Global Symmetry: Cyclic - C2 (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2
Find Similar Assemblies
Biological assembly 3 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 38.97 kDa
- Atom Count: 2,618
- Modeled Residue Count: 330
- Deposited Residue Count: 350
- Unique protein chains: 1
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| C-C MOTIF CHEMOKINE 3 | 70 | Homo sapiens | Mutation(s): 0 | 👁 Image | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P10147 (Homo sapiens) Explore P10147 Go to UniProtKB: P10147 | |||||
PHAROS: P10147 GTEx: ENSG00000277632 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P10147 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.65 Å
- R-Value Free: 0.265 (Depositor), 0.265 (DCC)
- R-Value Work: 0.223 (Depositor), 0.230 (DCC)
- R-Value Observed: 0.235 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 181.541 | α = 90 |
| b = 181.541 | β = 90 |
| c = 76.845 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| PHASER | phasing |
Revision History (Full details and data files)
- Version 1.0: 2010-11-03
Type: Initial release - Version 1.1: 2011-05-08
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Version format compliance - Version 1.3: 2024-11-06
Changes: Data collection, Database references, Other, Structure summary
