7THB | pdb_00007thb

Crystal structure of an RNA-5'/DNA-3' strand exchange junction

• PDB DOI: https://doi.org/10.2210/pdb7THB/pdb
• NAKB: 7THB

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


• Deposited: 2022-01-10 Released: 2022-04-27 
• Deposition Author(s): Cofsky, J.C., Knott, G.J., Gee, C.L., Doudna, J.A.
• Funding Organization(s): National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free: 
  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of an RNA/DNA strand exchange junction.

Cofsky, J.C., Knott, G.J., Gee, C.L., Doudna, J.A.

(2022) PLoS One 17: e0263547-e0263547

• PubMed: 35436289 
• DOI: https://doi.org/10.1371/journal.pone.0263547
• Primary Citation Related Structures: 
  7THB


• PubMed Abstract: 
  

  Short segments of RNA displace one strand of a DNA duplex during diverse processes including transcription and CRISPR-mediated immunity and genome editing. These strand exchange events involve the intersection of two geometrically distinct helix types-an RNA:DNA hybrid (A-form) and a DNA:DNA homoduplex (B-form). Although previous evidence suggests that these two helices can stack on each other, it is unknown what local geometric adjustments could enable A-on-B stacking. Here we report the X-ray crystal structure of an RNA-5'/DNA-3' strand exchange junction at an anisotropic resolution of 1.6 to 2.2 Å. The structure reveals that the A-to-B helical transition involves a combination of helical axis misalignment, helical axis tilting and compression of the DNA strand within the RNA:DNA helix, where nucleotides exhibit a mixture of A- and B-form geometry. These structural principles explain previous observations of conformational stability in RNA/DNA exchange junctions, enabling a nucleic acid architecture that is repeatedly populated during biological strand exchange events.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America.
Department of Biochemistry & Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California, United States of America.
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, California, United States of America.
Department of Chemistry, University of California, Berkeley, Berkeley, California, United States of America.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, Berkeley, California, United States of America.
Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, United States of America.
Gladstone Institutes, University of California, San Francisco, San Francisco, California, United States of America.

Biological Assembly 1  

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

Biological Assembly 2  

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 23.9 kDa 
• Atom Count: 1,651 
• Modeled Residue Count: 78 
• Deposited Residue Count: 78 
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*AP*AP*GP*CP*AP*GP*CP*AP*TP*C)-3')	A, D, G	12	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*AP*GP*CP*UP*UP*AP*C)-3')	B, E, H	7	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*TP*GP*CP*TP*C)-3')	C, F, I	7	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.64 Å
• R-Value Free:  0.284 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37THB

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.025	α = 92.056
b = 43.586	β = 103.722
c = 52.182	γ = 99.952

Software Package:

Software Name	Purpose
XDS	data reduction
STARANISO	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Cofsky, J.C., Knott, G.J., Gee, C.L., Doudna, J.A.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1817593
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection
• Version 1.2: 2024-04-03
  Changes: Refinement description