2QZ4

Human paraplegin, AAA domain in complex with ADP

• PDB DOI: https://doi.org/10.2210/pdb2QZ4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-08-16 Released: 2007-09-11 
• Deposition Author(s): Karlberg, T., Lehtio, L., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, J., Sagemark, C., Sundstrom, M., Thorsell, A.G., Tresauges, L., Van Den Berg, S., Weigelt, J., Welin, M., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

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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 

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

• PubMed: 19841671 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28.98 kDa 
• Atom Count: 1,762 
• Modelled Residue Count: 223 
• Deposited Residue Count: 262 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Paraplegin	A	262	Homo sapiens	Mutation(s): 0  Gene Names: SPG7 EC: 3.4.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UQ90 (Homo sapiens) Explore Q9UQ90  Go to UniProtKB:  Q9UQ90
PHAROS:  Q9UQ90 GTEx:  ENSG00000197912

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	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 = 57.2	α = 90
b = 57.2	β = 90
c = 155.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DNA	data collection
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Karlberg, T., Lehtio, L., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Herman, M.D., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, J., Sagemark, C., Sundstrom, M., Thorsell, A.G., Tresauges, L., Van Den Berg, S., Weigelt, J., Welin, M., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Revision History  

• 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