Summary information

PDB id
1phj
Class
DNA binding protein-DNA
Method
X-ray (2.5 Å)
Summary
Crystal structure of the oxytricha nova telomere end-binding protein complexed with noncognate ssDNA gg(3dr)gttttgggg
Reference
Theobald DL, Schultz SC (2003): "Nucleotide Shuffling and ssDNA Recognition in Oxytricha Nova Telomere End-Binding Protein Complexes." Embo J., 22, 4314-4324. doi: 10.1093/emboj/cdg415.
Abstract
Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.
G4 notes
4 G-tetrads, 1 G4 helix, 1 G4 stem, (2+2), UDDU

Base-block schematics in six views

PyMOL session file PDB file View in 3Dmol.js

List of 4 G-tetrads

 1 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.308 type=bowl   nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.177 type=other  nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3 glyco-bond=s--s sugar=---- groove=w-n- planarity=0.173 type=other  nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4 glyco-bond=-ss- sugar=---- groove=w-n- planarity=0.299 type=bowl   nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12

List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem.

Helix#1, 4 G-tetrad layers, inter-molecular, with 1 stem

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
  step#1  mm(<>,outward)  area=13.98 rise=3.48 twist=17.1
  step#2  pp(><,inward)   area=14.93 rise=3.51 twist=36.6
  step#3  mm(<>,outward)  area=12.73 rise=3.42 twist=18.1
  strand#1 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG G.DG1,G.DG2,G.DG3,G.DG4
  strand#2 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG H.DG4,H.DG3,H.DG2,H.DG1
  strand#3 DNA glyco-bond=-s-s sugar=---- nts=4 GGGG G.DG12,G.DG11,G.DG10,G.DG9
  strand#4 DNA glyco-bond=s-s- sugar=---- nts=4 GGGG H.DG9,H.DG10,H.DG11,H.DG12

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3 stacking diagrams 
 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
  step#1  mm(<>,outward)  area=13.98 rise=3.48 twist=17.1

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 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
  step#2  pp(><,inward)   area=14.93 rise=3.51 twist=36.6

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 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
  step#3  mm(<>,outward)  area=12.73 rise=3.42 twist=18.1

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List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands.

Stem#1, 4 G-tetrad layers, 2 loops, inter-molecular, UDDU, anti-parallel, (2+2)

 1  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG1,H.DG4,G.DG12,H.DG9
 2  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG2,H.DG3,G.DG11,H.DG10
 3  glyco-bond=s--s sugar=---- groove=w-n- Major-->WC nts=4 GGGG G.DG3,H.DG2,G.DG10,H.DG11
 4  glyco-bond=-ss- sugar=---- groove=w-n- WC-->Major nts=4 GGGG G.DG4,H.DG1,G.DG9,H.DG12
  step#1  mm(<>,outward)  area=13.98 rise=3.48 twist=17.1
  step#2  pp(><,inward)   area=14.93 rise=3.51 twist=36.6
  step#3  mm(<>,outward)  area=12.73 rise=3.42 twist=18.1
  strand#1  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG G.DG1,G.DG2,G.DG3,G.DG4
  strand#2  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG H.DG4,H.DG3,H.DG2,H.DG1
  strand#3  D DNA glyco-bond=-s-s sugar=---- nts=4 GGGG G.DG12,G.DG11,G.DG10,G.DG9
  strand#4  U DNA glyco-bond=s-s- sugar=---- nts=4 GGGG H.DG9,H.DG10,H.DG11,H.DG12
  loop#1 type=diagonal  strands=[#1,#3] nts=4 TTTT G.DT5,G.DT6,G.DT7,G.DT8
  loop#2 type=diagonal  strands=[#2,#4] nts=4 TTTT H.DT5,H.DT6,H.DT7,H.DT8

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