2YPT

Crystal structure of the human nuclear membrane zinc metalloprotease ZMPSTE24 mutant (E336A) in complex with a synthetic CSIM tetrapeptide from the C-terminus of prelamin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.263 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structural Basis of Zmpste24-Dependent Laminopathies.

Quigley, A.Dong, Y.Y.Pike, A.C.W.Dong, L.Shrestha, L.Berridge, G.Stansfeld, P.J.Sansom, M.S.P.Edwards, A.M.Bountra, C.von Delft, F.Bullock, A.N.Burgess-Brown, N.A.Carpenter, E.P.

(2013) Science 339: 1604

  • DOI: 10.1126/science.1231513
  • Primary Citation of Related Structures:  4AW6

  • PubMed Abstract: 
  • Mutations in the nuclear membrane zinc metalloprotease ZMPSTE24 lead to diseases of lamin processing (laminopathies), such as the premature aging disease progeria and metabolic disorders. ZMPSTE24 processes prelamin A, a component of the nuclear lami ...

    Mutations in the nuclear membrane zinc metalloprotease ZMPSTE24 lead to diseases of lamin processing (laminopathies), such as the premature aging disease progeria and metabolic disorders. ZMPSTE24 processes prelamin A, a component of the nuclear lamina intermediate filaments, by cleaving it at two sites. Failure of this processing results in accumulation of farnesylated, membrane-associated prelamin A. The 3.4 angstrom crystal structure of human ZMPSTE24 has a seven transmembrane α-helical barrel structure, surrounding a large, water-filled, intramembrane chamber, capped by a zinc metalloprotease domain with the catalytic site facing into the chamber. The 3.8 angstrom structure of a complex with a CSIM tetrapeptide showed that the mode of binding of the substrate resembles that of an insect metalloprotease inhibitor in thermolysin. Laminopathy-associated mutations predicted to reduce ZMPSTE24 activity map to the zinc metalloprotease peptide-binding site and to the bottom of the chamber.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAAX PRENYL PROTEASE 1 HOMOLOG
A, B, D, E
482Homo sapiensGene Names: ZMPSTE24 (FACE1, STE24)
EC: 3.4.24.84
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Intramembrane Proteases
Protein: 
CAAX protease ZMPSTE24
Find proteins for O75844 (Homo sapiens)
Go to Gene View: ZMPSTE24
Go to UniProtKB:  O75844
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PRELAMIN-A/C
F, G, H, I
4Homo sapiensGene Names: LMNA (LMN1)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Intramembrane Proteases
Protein: 
CAAX protease ZMPSTE24
Find proteins for P02545 (Homo sapiens)
Go to Gene View: LMNA
Go to UniProtKB:  P02545
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.263 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 61.320α = 76.26
b = 95.540β = 79.67
c = 132.030γ = 72.30
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-05-15
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Database references, Structure summary