6RUP

Human mitochondrial single-stranded DNA binding protein, SSBP1, at 2.1 A resolution - elucidated sequence


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Dominant mutations in mtDNA maintenance gene SSBP1 cause optic atrophy and foveopathy.

Piro-Megy, C.Sarzi, E.Tarres-Sole, A.Pequignot, M.Hensen, F.Quiles, M.Manes, G.Chakraborty, A.Senechal, A.Bocquet, B.Cazevieille, C.Roubertie, A.Muller, A.Charif, M.Goudenege, D.Lenaers, G.Wilhelm, H.Kellner, U.Weisschuh, N.Wissinger, B.Zanlonghi, X.Hamel, C.Spelbrink, J.N.Sola, M.Delettre, C.

(2019) J.Clin.Invest. --: --

  • DOI: 10.1172/JCI128513

  • PubMed Abstract: 
  • Mutations in genes encoding components of the mitochondrial DNA (mtDNA) replication machinery cause mtDNA depletion syndromes (MDS), which associate ocular features with severe neurological syndromes. Here, we identified heterozygous missense mutatio ...

    Mutations in genes encoding components of the mitochondrial DNA (mtDNA) replication machinery cause mtDNA depletion syndromes (MDS), which associate ocular features with severe neurological syndromes. Here, we identified heterozygous missense mutations in SSBP1 in five unrelated families, leading to the R38Q and R107Q amino-acid changes in the mitochondrial single-stranded DNA-binding protein, a crucial protein involved in mtDNA replication. All affected individuals presented optic atrophy, associated with foveopathy in half of the cases. To uncover the structural features underlying SSBP1 mutations, we determined a new revised SSBP1 crystal structure. Structural analysis suggests that both mutations affect dimer interactions and presumably distort the DNA binding region. Using patient fibroblasts, we validated that the R38Q variant destabilizes SSBP1 dimer/tetramer formation, affects mtDNA replication and induces mtDNA depletion. Our study, showing that mutations in SSBP1 cause a novel form of dominant optic atrophy frequently accompanied with foveopathy, brings new insights into mtDNA maintenance disorders.


    Related Citations: 
    • Mitochondrial RNA granules are critically dependent on mtDNA replication factors Twinkle and mtSSB.
      Hensen, F.,Potter, A.,van Esveld, S.L.,Tarres-Sole, A.,Chakraborty, A.,Sola, M.,Spelbrink, J.N.
      (2019) Nucleic Acids Res. 47: 3680



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Single-stranded DNA-binding protein, mitochondrial
A, B
142Homo sapiensMutation(s): 0 
Gene Names: SSBP1 (SSBP)
Find proteins for Q04837 (Homo sapiens)
Go to Gene View: SSBP1
Go to UniProtKB:  Q04837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SER-SER-SER-SER
C
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.200 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.040α = 90.00
b = 51.040β = 90.00
c = 182.340γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpain--

Revision History 

  • Version 1.0: 2019-10-09
    Type: Initial release