Biological Assembly 1  

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Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 7572.72 
• Atom Count: 538 
• Residue Count: 24 
• Unique nucleic acid chains: 2

3SSF

Crystal structure of RNA:DNA dodecamer corresponding to HIV-1 polypurine tract, at 1.6 A resolution.

• DOI: 10.2210/pdb3SSF/pdb
• NDB: NA1220

• Classification: RNA/DNA


• Deposited: 2011-07-08 Released: 2012-02-08 
• Deposition Author(s): Drozdzal, P., Michalska, K., Kierzek, R., Lomozik, L., Jaskolski, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 

Literature

Structure of an RNA/DNA dodecamer corresponding to the HIV-1 polypurine tract at 1.6 Angstrom resolution

Drozdzal, P., Michalska, K., Kierzek, R., Lomozik, L., Jaskolski, M.

(2012) Acta Crystallogr.,Sect.D 68: 169-175

• PubMed: 22281746 
• DOI: 10.1107/S0907444911053327


• PubMed Abstract: 
  

The crystal structure of an RNA/DNA hybrid dodecamer, r(5'-uaaaagaaaagg):d(5'-CCTTTTCTTTTA), which contains three-quarters of the polypurine tract (PPT) sequence of the HIV RNA genome is reported. The hybrid structure was determined at 1.6 Å resolution and was found to have the A-form conformation. However, the presence of alternate conformations along the RNA template strand indicated increased flexibility of the PPT sequence. Two segments (at nucleotides 1-2 and 6-8) of the RNA chain have two conformations exhibiting differences in torsion and pseudorotation angles. For conformation I((1-2), (6-8)), 25% of the RNA sugars have the C2'-exo pucker and the rest have the expected C3'-endo pucker. The II(1-2) and II(6-8) conformations of the RNA strand have one sugar with the C2'-exo pucker. None of the ribose rings exist in the C2'-endo form, in contrast to a previous report which postulated a C2'-endo ribose as a key structural element of the PPT. The widths of the minor groove for conformations I((1-2), (6-8)) and II((1-2), (6-8)) of the RNA strand are 9.2-10.5 and 9.4-10.7 Å, respectively. Both ranges are very close to the intervals accepted for A-form RNA duplexes. On the opposing DNA primer strand most of the sugars are C3'-endo, except for the 3'-terminal sugars, which are C2'-endo (T22) or O4'-endo (T23 and A24). The duplex includes a noncanonical u1(anti)·A24(syn) base interaction with only one hydrogen bond between the bases. This noncanonical base interaction at the 5'-end of the template distorts the values of the helical parameters of the adjacent base pair.

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Related Citations: 

• An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H.
  Kopka, M.L.,Lavelle, L.,Han, G.W.,Ng, H.-L.,Dickerson, R.E.
  (2003) J.Mol.Biol. 334: 653
• Crystal structure of an RNA.DNA hybrid reveals intermolecular intercalation: dimer formation by base-pair swapping.
  Han, G.W.,Kopka, M.L.,Langs, D.,Sawaya, M.R.,Dickerson, R.E.
  (2003) Proc.Natl.Acad.Sci.USA 100: 9214
• Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA
  G Sarafianos, S.,Das, K.,Tantillo, C.,Clark Jr., A.D.,Ding, J.,Whitcomb, J.M.,Boyer, P.L.,Hughes, S.H.,Arnold, E.
  (2001) Embo J. 20: 1449




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Organizational Affiliation: 

Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Length	Organism
5'-R(*UP*AP*AP*AP*AP*GP*AP*AP*AP*AP*GP*G)-3'	A	12	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*CP*CP*TP*TP*TP*TP*CP*TP*TP*TP*TP*A)-3'	B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 41.904	α = 90.00
b = 41.904	β = 90.00
c = 57.240	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-07-08 
• Released Date: 2012-02-08 
• Deposition Author(s): Drozdzal, P., Michalska, K., Kierzek, R., Lomozik, L., Jaskolski, M.

Revision History 

• Version 1.0: 2012-02-08
  Type: Initial release
• Version 1.1: 2012-03-28
  Type: Database references