9RK6 | pdb_00009rk6

Paraplegin N-terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.296 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.239 (DCC) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9RK6

This is version 1.1 of the entry. See complete history

Literature

Structural divergence in N-terminal domains of AAA proteases paraplegin (SPG7) and FtsH indicates a key structural function in complex formation.

Hyatt, J.G.Paterson, N.G.Devos, J.M.Oliveira, C.L.P.Jessen, C.M.Prevost, S.Hofmann, A.Pedersen, J.S.Winter, A.

(2026) J Struct Biol 218: 108353-108353

  • DOI: https://doi.org/10.1016/j.jsb.2026.108353
  • Primary Citation Related Structures: 
    9RK6

  • PubMed Abstract: 

    AAA proteases are hexameric ATP-dependent metallopeptidases that perform crucial proteolytic activities within prokaryotic and eukaryotic membranes. Structurally, protomers are comprised of catalytically active C-terminal domains that are anchored to the membrane by an N-terminal autonomous folding unit. In this study, we determined the fold, stability, and oligomeric state of the N-terminal intermembrane domains of human spastic paraplegia type 7 (SPG7)/ paraplegin protein and its bacterial orthologue FtsH using circular dichroism (CD), small-angle X-ray scattering (SAXS), small-angle neutron scattering (SANS) and X-ray crystallography. Solution-state analysis revealed that the N-terminal domain of paraplegin is a monomer in solution whereas FtsH predominantly forms a dimer. Unexpectedly, the N-terminal domain of paraplegin presents as a domain-swapped homodimer in our crystal structure that involves the first helix and first two beta-strands from one monomer and beta-strand 3, helix 2 and beta-strand 4 from another symmetry-related molecule. However, together they form an assembly which is similar to protomers observed for the N-terminal regions of FtsH and AFG3L2. Drawing from our structural data, we postulate that domain-swapping interactions of the N-terminal regions contribute to stability of the AAA protease hexamer containing paraplegin, demonstrating the extensive flexibility of the N-terminal portion of this protein and its role in achieving the appropriate molecular architecture required for function.


  • Organizational Affiliation
    • School of Life Sciences, Keele University, Huxley Building, Keele, Staffordshire ST5 5BG, UK.

Macromolecule Content 

  • Total Structure Weight: 20.01 kDa 
  • Atom Count: 1,475 
  • Modeled Residue Count: 169 
  • Deposited Residue Count: 174 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Mitochondrial inner membrane m-AAA protease component parapleginA [auth B],
B [auth A]
87Homo sapiensMutation(s): 0 
Gene Names: SPG7CARCMARPGN
EC: 3.4.24 (PDB Primary Data), 3.6 (PDB Primary Data)
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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.296 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.239 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.393α = 90
b = 63.844β = 90
c = 99.813γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-24
    Type: Initial release
  • Version 1.1: 2026-08-19
    Changes: Database references