398D | pdb_0000398d

3'-DNA-RNA-5' JUNCTION FORMED DURING INITIATION OF MINUS-STRAND SYNTHESIS OF HIV REPLICATION

• PDB DOI: https://doi.org/10.2210/pdb398D/pdb
• NAKB: 398D

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


• Deposited: 1998-05-04 Released: 1998-10-06 
• Deposition Author(s): Mueller, U., Meier, G., Mochi-Onori, A., Cellai, L., Heumann, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.291 (Depositor), 0.301 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.234 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of an eight-base pair duplex containing the 3'-DNA-RNA-5' junction formed during initiation of minus-strand synthesis of HIV replication.

Mueller, U., Maier, G., Mochi Onori, A., Cellai, L., Heumann, H., Heinemann, U.

(1998) Biochemistry 37: 12005-12011

• PubMed: 9724510 
• DOI: https://doi.org/10.1021/bi981152y
• Primary Citation Related Structures: 
  398D


• PubMed Abstract: 
  

  During initiation of minus-strand synthesis by HIV-1 reverse transcriptase, a 3'-DNA-RNA-5' junction is formed involving the 3'-end of tRNAlys,3. The HIV-RT-associated RNase H cleaves the RNA template strand specifically, opposite the newly synthesized DNA strand. We have determined the crystal structure at 1.9 A resolution of an eight-base pair hybrid duplex representing the junction to identify global or local structural perturbations which may be recognized by HIV-RT RNase H. The junction octamer is in a global A-type conformation throughout. A base pair step with distinct stacking geometry and variable backbone conformation is located next to the main endonucleolytic cleavage site. This base pair step may serve as a recognition site for HIV-RT RNase H.

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Organizational Affiliation: 
• Forschungsgruppe Kristallographie, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.07 kDa 
• Atom Count: 750 
• Modeled Residue Count: 32 
• Deposited Residue Count: 32 
• Unique nucleic acid chains: 1
• Unique hybrid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*CP*AP*GP*UP*GP*GP*C)-3')	A, C	8	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA/RNA (5'-R(*GP*CP*CP*AP)-D(*CP*TP*GP*C)-3')	B, D	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.291 (Depositor), 0.301 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.234 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.74	α = 90
b = 44.15	β = 90
c = 51.93	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-06 
Deposition Author(s): Mueller, U., Meier, G., Mochi-Onori, A., Cellai, L., Heumann, H.

Revision History  

• Version 1.0: 1998-10-06
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references
• Version 1.4: 2024-04-03
  Changes: Refinement description