3ULL

HUMAN MITOCHONDRIAL SINGLE-STRANDED DNA BINDING PROTEIN

• PDB DOI: https://doi.org/10.2210/pdb3ULL/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1996-12-11 Released: 1997-10-15 
• Deposition Author(s): Yang, C., Curth, U., Urbanke, C., Kang, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 

Literature

Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution.

Yang, C., Curth, U., Urbanke, C., Kang, C.

(1997) Nat Struct Biol 4: 153-157

• PubMed: 9033597 
• DOI: https://doi.org/10.1038/nsb0297-153
• Primary Citation of Related Structures:  
  3ULL


• PubMed Abstract: 
  

  We solved the crystal structure of the homotetrameric single-stranded DNA binding (SSB) protein from human mitochondria at a resolution of 2.4 A. The tetramer is formed by two dimers interacting head-to-head and shows D2 symmetry. Sequence-related tetrameric SSB proteins occur in prokaryotes and eukaryotic mitochondria; this is the first report of an atomic resolution structure of this type of protein. Using biochemical data and analysis of sequence homologies, we were able to correlate the functional properties with structure. We propose that ssDNA wraps around the tetrameric HsmtSSB protein through electropositive channels guided by flexible loops.

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Organizational Affiliation: 

Department of Biochemistry and Biophysics, Washington State University, Pullman 99164-4660, USA.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 30.43 kDa 
• Atom Count: 1,756 
• Modelled Residue Count: 209 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA BINDING PROTEIN	A, B	132	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q04837 (Homo sapiens) Explore Q04837  Go to UniProtKB:  Q04837
PHAROS:  Q04837 GTEx:  ENSG00000106028

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.195 
• R-Value Observed: 0.195 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.83	α = 90
b = 51.83	β = 90
c = 184.24	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
X-PLOR	model building
X-PLOR	refinement
bioteX	data reduction
bioteX	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-10-15 
Deposition Author(s): Yang, C., Curth, U., Urbanke, C., Kang, C.

Revision History  

• Version 1.0: 1997-10-15
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Refinement description, Structure summary