VOOZH about

URL: https://www.rcsb.org/structure/2X6G

⇱ RCSB PDB - 2X6G: X-ray Structure of Macrophage Inflammatory Protein-1 alpha (D27A)


👁 RCSB PDB
251,806
Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)

 2X6G | pdb_00002x6g

X-ray Structure of Macrophage Inflammatory Protein-1 alpha (D27A)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 
    0.286 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

wwPDB Validation  3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

  • PubMed20959807 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.


  • Organizational Affiliation
    • Ben-May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.

Macromolecule Content 

  • Total Structure Weight: 139.49 kDa 
  • Atom Count: 9,591 
  • Modeled Residue Count: 1,158 
  • Deposited Residue Count: 1,260 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
C-C MOTIF CHEMOKINE 3
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
70Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10147
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free:  0.286 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.211α = 90
b = 113.527β = 90
c = 173.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report

👁 Image


Entry History 

Deposition Data

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: 2024-10-16
    Changes: Data collection, Database references, Other, Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.