2QZ4

Human paraplegin, AAA domain in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the ATPase Domain of the Human AAA+ Protein Paraplegin/SPG7.

Karlberg, T.van den Berg, S.Hammarstrom, M.Sagemark, J.Johansson, I.Holmberg-Schiavone, L.Schuler, H.

(2009) PLoS One 4: e6975-e6975

  • DOI: https://doi.org/10.1371/journal.pone.0006975
  • Primary Citation of Related Structures:  
    2QZ4

  • PubMed Abstract: 

    Paraplegin is an m-AAA protease of the mitochondrial inner membrane that is linked to hereditary spastic paraplegias. The gene encodes an FtsH-homology protease domain in tandem with an AAA+ homology ATPase domain. The protein is believed to form a hexamer that uses ATPase-driven conformational changes in its AAA-domain to deliver substrate peptides to its protease domain. We present the crystal structure of the AAA-domain of human paraplegin bound to ADP at 2.2 A. This enables assignment of the roles of specific side chains within the catalytic cycle, and provides the structural basis for understanding the mechanism of disease mutations. This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3D representations and animated transitions. Please note that a web plugin is required to access this enhanced functionality. Instructions for the installation and use of the web plugin are available in Text S1.


  • Organizational Affiliation

    Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Paraplegin262Homo sapiensMutation(s): 0 
Gene Names: SPG7
EC: 3.4.24 (PDB Primary Data), 3.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ90 (Homo sapiens)
Explore Q9UQ90 
Go to UniProtKB:  Q9UQ90
PHAROS:  Q9UQ90
GTEx:  ENSG00000197912 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UQ90
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.212 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.2α = 90
b = 57.2β = 90
c = 155.22γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DNAdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description