1OTC | pdb_00001otc

THE O. NOVA TELOMERE END BINDING PROTEIN COMPLEXED WITH SINGLE STRAND DNA

• PDB DOI: https://doi.org/10.2210/pdb1OTC/pdb
• NAKB: 1OTC

• Classification: PROTEIN/DNA
• Organism(s): Sterkiella nova
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-11-25 Released: 1999-04-12 
• Deposition Author(s): Horvath, M.P., Schweiker, V.L., Bevilacqua, J.M., Ruggles, J.A., Schultz, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.292 (Depositor), 0.286 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.241 (DCC) 
• R-Value Observed: 
  0.251 (Depositor) 

Literature

Crystal structure of the Oxytricha nova telomere end binding protein complexed with single strand DNA.

Horvath, M.P., Schweiker, V.L., Bevilacqua, J.M., Ruggles, J.A., Schultz, S.C.

(1998) Cell 95: 963-974

• PubMed: 9875850 
• DOI: https://doi.org/10.1016/s0092-8674(00)81720-1
• Primary Citation Related Structures: 
  1OTC


• PubMed Abstract: 
  

  Telomeres are specialized protein-DNA complexes that compose the ends of eukaryotic chromosomes. Telomeres protect chromosome termini from degradation and recombination and act together with telomerase to ensure complete genome replication. We have determined the crystal structure of the two-subunit Oxytricha nova telomere end binding protein (OnTEBP) complexed with single strand telomeric DNA at 2.8 A resolution. The structure reveals four oligonucleotide/oligosaccharide-binding folds, three of which form a deep cleft that binds the ssDNA, and a fourth that forms an unusual protein-protein interaction between the alpha and beta subunits. This structure provides a molecular description of how the two subunits of OnTEBP recognize and bind ssDNA to form a sequence-specific, telomeric nucleoprotein complex that caps the very 3' ends of chromosomes.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 88.69 kDa 
• Atom Count: 5,680 
• Modeled Residue Count: 684 
• Deposited Residue Count: 767 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TELOMERE-BINDING PROTEIN ALPHA SUBUNIT)	B [auth A]	495	Sterkiella nova	Mutation(s): 0  Gene Names: MAC-56A
UniProt
Find proteins for P29549 (Sterkiella nova) Explore P29549  Go to UniProtKB:  P29549

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (TELOMERE-BINDING PROTEIN BETA SUBUNIT)	C [auth B]	260	Sterkiella nova	Mutation(s): 0  Gene Names: MAC-41A
UniProt
Find proteins for P16458 (Sterkiella nova) Explore P16458  Go to UniProtKB:  P16458

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*G)-3')	A [auth D]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.292 (Depositor), 0.286 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.241 (DCC) 
• R-Value Observed: 0.251 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.5	α = 90
b = 94.5	β = 90
c = 426.2	γ = 120

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-12 
Deposition Author(s): Horvath, M.P., Schweiker, V.L., Bevilacqua, J.M., Ruggles, J.A., Schultz, S.C.

Revision History  

• Version 1.0: 1999-04-12
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references