7Q6J | pdb_00007q6j

Crystal structure of the human GDAP1 CMT2 mutant-H123R


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structural insights into Charcot-Marie-Tooth disease-linked mutations in human GDAP1.

Sutinen, A.Nguyen, G.T.T.Raasakka, A.Muruganandam, G.Loris, R.Ylikallio, E.Tyynismaa, H.Bartesaghi, L.Ruskamo, S.Kursula, P.

(2022) FEBS Open Bio 12: 1306-1324

  • DOI: https://doi.org/10.1002/2211-5463.13422
  • Primary Citation Related Structures: 
    7Q6J, 7Q6K, 7YWD

  • PubMed Abstract: 

    Charcot-Marie-Tooth disease (CMT) is the most common inherited peripheral polyneuropathy in humans, and its different subtypes are linked to mutations in dozens of different genes. Mutations in ganglioside-induced differentiation-associated protein 1 (GDAP1) cause two types of CMT, demyelinating CMT4A and axonal CMT2K. The GDAP1-linked CMT genotypes are mainly missense point mutations. Despite clinical profiling and in vivo studies on the mutations, the etiology of GDAP1-linked CMT is poorly understood. Here, we describe the biochemical and structural properties of the Finnish founding CMT2K mutation H123R and CMT2K-linked R120W, both of which are autosomal dominant mutations. The disease variant proteins retain close to normal structure and solution behavior, but both present a significant decrease in thermal stability. Using GDAP1 variant crystal structures, we identify a side-chain interaction network between helices ⍺3, ⍺6, and ⍺7, which is affected by CMT mutations, as well as a hinge in the long helix ⍺6, which is linked to structural flexibility. Structural analysis of GDAP1 indicates that CMT may arise from disruption of specific intra- and intermolecular interaction networks, leading to alterations in GDAP1 structure and stability, and, eventually, insufficient motor and sensory neuron function.


  • Organizational Affiliation
    • Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.

Macromolecule Content 

  • Total Structure Weight: 65.8 kDa 
  • Atom Count: 4,339 
  • Modeled Residue Count: 505 
  • Deposited Residue Count: 560 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ganglioside-induced differentiation-associated protein 1
A, B
280Homo sapiensMutation(s): 1 
Gene Names: GDAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TB36 (Homo sapiens)
Explore Q8TB36 
Go to UniProtKB:  Q8TB36
PHAROS:  Q8TB36
GTEx:  ENSG00000104381 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TB36
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.71α = 90
b = 115.88β = 90
c = 116.18γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland24302881

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-07-13
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary