421D

5'-D(*TP*TP*CP*TP*TP*(BRO)CP*TP*TP*C)-3', 5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3'

• PDB DOI: https://doi.org/10.2210/pdb421D/pdb
• NAKB: 421D

• Classification: DNA-RNA HYBRID
• Mutation(s): No 


• Deposited: 1998-08-16 Released: 1999-01-05 
• Deposition Author(s): Xiong, Y., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 

Literature

Crystal structure and conformation of a DNA-RNA hybrid duplex with a polypurine RNA strand: d(TTCTTBr5CTTC)-r(GAAGAAGAA).

Xiong, Y., Sundaralingam, M.

(1998) Structure 6: 1493-1501

• PubMed: 9862803 
• DOI: https://doi.org/10.1016/s0969-2126(98)00148-8
• Primary Citation of Related Structures:  
  421D


• PubMed Abstract: 
  

  . DNA-RNA hybrids are substrates for RNase H. This enzyme catalyzes the hydrolysis of the RNA strand in the hybrid form. The polypurine tract (PPT) in human immunodeficiency virus 1 (HIV-1) is a short stretch of purines ( approximately 15 bases) located at the 3'-end of the U3 region of the RNA genome. The PPT has the unique ability to resist digestion by RNase H and serves as a primer for plus-strand DNA synthesis.

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Organizational Affiliation: 

The Ohio State University Biological Macromolecular Structure Center Departments of Chemistry, Biochemistry and Biophysics Program 012 Rightmire Hall 1060 Carmack Road Columbus Ohio 43210 USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.69 kDa 
• Atom Count: 413 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*CP*TP*TP*(CBR)P*TP*TP*C)-3')	A	9	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*AP*AP*GP*AP*AP*GP*AP*A)-3')	B	9	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.237 
• R-Value Work: 0.201 
• R-Value Observed: 0.201 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.08	α = 90
b = 48.08	β = 90
c = 42.88	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-05 
Deposition Author(s): Xiong, Y., Sundaralingam, M.

Revision History  

• Version 1.0: 1999-01-05
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations