4RAL

Crystal structure of insulin degrading enzyme in complex with macrophage inflammatory protein 1 beta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.148 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of human CCL18, CCL3, and CCL4 reveal molecular determinants for quaternary structures and sensitivity to insulin-degrading enzyme.

Liang, W.G.Ren, M.Zhao, F.Tang, W.J.

(2015) J.Mol.Biol. 427: 1345-1358

  • DOI: 10.1016/j.jmb.2015.01.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • CC chemokine ligands (CCLs) are 8- to 14-kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic ...

    CC chemokine ligands (CCLs) are 8- to 14-kDa signaling proteins involved in diverse immune functions. While CCLs share similar tertiary structures, oligomerization produces highly diverse quaternary structures that protect chemokines from proteolytic degradation and modulate their functions. CCL18 is closely related to CCL3 and CCL4 with respect to both protein sequence and genomic location, yet CCL18 has distinct biochemical and biophysical properties. Here, we report a crystal structure of human CCL18 and its oligomerization states in solution based on crystallographic and small-angle X-ray scattering analyses. Our data show that CCL18 adopts an α-helical conformation at its N-terminus that weakens its dimerization, explaining CCL18's preference for the monomeric state. Multiple contacts between monomers allow CCL18 to reversibly form a unique open-ended oligomer different from those of CCL3, CCL4, and CCL5. Furthermore, these differences hinge on proline 8, which is conserved in CCL3 and CCL4 but is replaced by lysine in human CCL18. Our structural analyses suggest that a mutation of proline 8 to alanine stabilizes a type 1 β-turn at the N-terminus of CCL4 to prevent dimerization but prevents dimers from making key contacts with each other in CCL3. Thus, the P8A mutation induces depolymerization of CCL3 and CCL4 by distinct mechanisms. Finally, we used structural, biochemical, and functional analyses to unravel why insulin-degrading enzyme degrades CCL3 and CCL4 but not CCL18. Our results elucidate the molecular basis for the oligomerization of three closely related CC chemokines and suggest how oligomerization shapes CCL chemokine function.


    Organizational Affiliation

    Ben-May Department for Cancer Research, The University of Chicago, IL 60637.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Insulin-degrading enzyme
A, B
990Homo sapiensMutation(s): 14 
Gene Names: IDE
EC: 3.4.24.56
Find proteins for P14735 (Homo sapiens)
Go to Gene View: IDE
Go to UniProtKB:  P14735
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-C motif chemokine 4
D, E
69Homo sapiensMutation(s): 0 
Gene Names: CCL4 (LAG1, MIP1B, SCYA4)
Find proteins for P13236 (Homo sapiens)
Go to Gene View: CCL4
Go to UniProtKB:  P13236
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.148 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.191 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 263.117α = 90.00
b = 263.117β = 90.00
c = 90.850γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data collection
PHASESphasing
HKL-3000data scaling
HKL-3000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release