7JY6

Analysis of a strand exchange reaction with a mini filament of 9-RecA, oligo(dT)27 primary ssDNA, non-homologous 120 bp dsDNA and ATPgammaS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanism of strand exchange from RecA-DNA synaptic and D-loop structures.

Yang, H.Zhou, C.Dhar, A.Pavletich, N.P.

(2020) Nature 586: 801-806

  • DOI: 10.1038/s41586-020-2820-9
  • Primary Citation of Related Structures:  
    7JY8, 7JY9, 7JY6, 7JY7

  • PubMed Abstract: 
  • The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This filament binds to a donor double-stranded DNA (dsDNA) to form synaptic filaments, which search for homology and then catalyse the exchange of the complementary strand, forming either a new heteroduplex or-if homology is limited-a D-loop 1,2 ...

    The strand-exchange reaction is central to homologous recombination. It is catalysed by the RecA family of ATPases, which form a helical filament with single-stranded DNA (ssDNA) and ATP. This filament binds to a donor double-stranded DNA (dsDNA) to form synaptic filaments, which search for homology and then catalyse the exchange of the complementary strand, forming either a new heteroduplex or-if homology is limited-a D-loop 1,2 . How synaptic filaments form, search for homology and catalyse strand exchange is poorly understood. Here we report the cryo-electron microscopy analysis of synaptic mini-filaments with both non-complementary and partially complementary dsDNA, and structures of RecA-D-loop complexes containing a 10- or a 12-base-pair heteroduplex. The C-terminal domain of RecA binds to dsDNA and directs it to the RecA L2 loop, which inserts into and opens up the duplex. The opening propagates through RecA sequestering the homologous strand at a secondary DNA-binding site, which frees the complementary strand to sample pairing with the ssDNA. At each RecA step, there is a roughly 20% probability that duplex opening will terminate and the as-yet-unopened dsDNA portion will bind to another C-terminal domain. Homology suppresses this process, through the cooperation of heteroduplex pairing with the binding of ssDNA to the secondary site, to extend dsDNA opening. This mechanism locally limits the length of ssDNA sampled for pairing if homology is not encountered, and could allow for the formation of multiple, widely separated synapses on the donor dsDNA, which would increase the likelihood of encountering homology. These findings provide key mechanistic insights into homologous recombination.


    Organizational Affiliation

    Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. pavletin@mskcc.org.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein RecA
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I
334Escherichia coliMutation(s): 0 
Gene Names: recANCTC11341_01072
UniProt
Find proteins for P0A7G6 (Escherichia coli (strain K12))
Explore P0A7G6 
Go to UniProtKB:  P0A7G6
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (27-MER)J [auth S]27Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (45-MER)K [auth U]45Escherichia coli
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
AA [auth H] , CA [auth I] , M [auth A] , O [auth B] , Q [auth C] , S [auth D] , U [auth E] , W [auth F] , 
AA [auth H],  CA [auth I],  M [auth A],  O [auth B],  Q [auth C],  S [auth D],  U [auth E],  W [auth F],  Y [auth G]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth I] , L [auth A] , N [auth B] , P [auth C] , R [auth D] , T [auth E] , V [auth F] , X [auth G] , 
BA [auth I],  L [auth A],  N [auth B],  P [auth C],  R [auth D],  T [auth E],  V [auth F],  X [auth G],  Z [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-08-29 
  • Released Date: 2020-11-04 
  • Deposition Author(s): Pavletich, N.P.

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-11
    Changes: Database references