1ICF

CRYSTAL STRUCTURE OF MHC CLASS II ASSOCIATED P41 II FRAGMENT IN COMPLEX WITH CATHEPSIN L


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of MHC class II-associated p41 Ii fragment bound to cathepsin L reveals the structural basis for differentiation between cathepsins L and S.

Guncar, G.Pungercic, G.Klemencic, I.Turk, V.Turk, D.

(1999) EMBO J. 18: 793-803

  • DOI: 10.1093/emboj/18.4.793

  • PubMed Abstract: 
  • The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifi ...

    The lysosomal cysteine proteases cathepsins S and L play crucial roles in the degradation of the invariant chain during maturation of MHC class II molecules and antigen processing. The p41 form of the invariant chain includes a fragment which specifically inhibits cathepsin L but not S. The crystal structure of the p41 fragment, a homologue of the thyroglobulin type-1 domains, has been determined at 2.0 A resolution in complex with cathepsin L. The structure of the p41 fragment demonstrates a novel fold, consisting of two subdomains, each stabilized by disulfide bridges. The first subdomain is an alpha-helix-beta-strand arrangement, whereas the second subdomain has a predominantly beta-strand arrangement. The wedge shape and three-loop arrangement of the p41 fragment bound to the active site cleft of cathepsin L are reminiscent of the inhibitory edge of cystatins, thus demonstrating the first example of convergent evolution observed in cysteine protease inhibitors. However, the different fold of the p41 fragment results in additional contacts with the top of the R-domain of the enzymes, which defines the specificity-determining S2 and S1' substrate-binding sites. This enables inhibitors based on the thyroglobulin type-1 domain fold, in contrast to the rather non-selective cystatins, to exhibit specificity for their target enzymes.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Jozcaronef Stefan Institute, Jamova 39, SLO-1000 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CATHEPSIN L: HEAVY CHAIN)
A, C
175Homo sapiensGene Names: CTSL (CTSL1)
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Go to Gene View: CTSL
Go to UniProtKB:  P07711
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CATHEPSIN L: LIGHT CHAIN)
B, D
42Homo sapiensGene Names: CTSL (CTSL1)
EC: 3.4.22.15
Find proteins for P07711 (Homo sapiens)
Go to Gene View: CTSL
Go to UniProtKB:  P07711
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (INVARIANT CHAIN)
I, J
65Homo sapiensGene Names: CD74 (DHLAG)
Find proteins for P04233 (Homo sapiens)
Go to Gene View: CD74
Go to UniProtKB:  P04233
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
I, J
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.592α = 90.00
b = 80.594β = 96.77
c = 64.245γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MAINrefinement
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-12
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance