8AMD | pdb_00008amd

Cryo-EM structure of the RecA presynaptic filament from S.pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb8AMD/pdb
• EM Map EMD-15524: EMDB EMDataResource
• NAKB: 8AMD

• Classification: RECOMBINATION
• Organism(s): Streptococcus pneumoniae, Bacteriophage sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-08-03 Released: 2023-03-22 
• Deposition Author(s): Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.
• Funding Organization(s): European Research Council (ERC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

Literature

Assembly mechanism and cryoEM structure of RecA recombination nucleofilaments from Streptococcus pneumoniae.

Hertzog, M., Perry, T.N., Dupaigne, P., Serres, S., Morales, V., Soulet, A.L., Bell, J.C., Margeat, E., Kowalczykowski, S.C., Le Cam, E., Fronzes, R., Polard, P.

(2023) Nucleic Acids Res 51: 2800-2817

• PubMed: 36806960 
• DOI: https://doi.org/10.1093/nar/gkad080
• Primary Citation Related Structures: 
  8AMD, 8AMF


• PubMed Abstract: 
  

  RecA-mediated homologous recombination (HR) is a key mechanism for genome maintenance and plasticity in bacteria. It proceeds through RecA assembly into a dynamic filament on ssDNA, the presynaptic filament, which mediates DNA homology search and ordered DNA strand exchange. Here, we combined structural, single molecule and biochemical approaches to characterize the ATP-dependent assembly mechanism of the presynaptic filament of RecA from Streptococcus pneumoniae (SpRecA), in comparison to the Escherichia coli RecA (EcRecA) paradigm. EcRecA polymerization on ssDNA is assisted by the Single-Stranded DNA Binding (SSB) protein, which unwinds ssDNA secondary structures that block EcRecA nucleofilament growth. We report by direct microscopic analysis of SpRecA filamentation on ssDNA that neither of the two paralogous pneumococcal SSBs could assist the extension of SpRecA nucleopolymers. Instead, we found that the conserved RadA helicase promotes SpRecA nucleofilamentation in an ATP-dependent manner. This allowed us to solve the atomic structure of such a long native SpRecA nucleopolymer by cryoEM stabilized with ATPγS. It was found to be equivalent to the crystal structure of the EcRecA filament with a marked difference in how RecA mediates nucleotide orientation in the stretched ssDNA. Then, our results show that SpRecA and EcRecA HR activities are different, in correlation with their distinct ATP-dependent ssDNA binding modes.

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Organizational Affiliation: 
• Laboratoire de Microbiologie et de Génétique Moléculaire (UMR 5100). Centre de Biologie Intégrative; 169, avenue Marianne Grunberg-Manago; CNRS - Université Paul Sabatier - Bât 4R4, 118, route de Narbonne; 31062 Toulouse cedex 09, France.
Structure and Function of Bacterial Nanomachines - Institut Européen de Chimie et Biologie, Microbiologie fondamentale et pathogénicité, UMR 5234, CNRS, University of Bordeaux, 2 rue Robert Escarpit, 33600 Pessac, France.
Genome Maintenance and Molecular Microscopy UMR 9019 CNRS, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex, France.
10x Genomics, Inc., Pleasanton, CA, USA.
CBS (Centre de Biologie Structurale), Univ Montpellier, CNRS, INSERM, Montpellier, France.
Department of Microbiology and Molecular Genetics and Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 173.73 kDa 
• Atom Count: 10,377 
• Modeled Residue Count: 1,344 
• Deposited Residue Count: 1,564 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein RecA	A, C [auth B], D [auth F], E [auth G]	388	Streptococcus pneumoniae	Mutation(s): 0  Gene Names: recA, spr1757
UniProt
Find proteins for P0A452 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore P0A452  Go to UniProtKB:  P0A452

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B [auth D]	12	Bacteriophage sp.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AGS (Subject of Investigation/LOI)	F [auth A], G [auth B], H [auth F], I [auth G]	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER C10 H16 N5 O12 P3 S NLTUCYMLOPLUHL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	2.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-03-22 
Deposition Author(s): Perry, T.N., Fronzes, R., Polard, P., Hertzog, M.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	725554

Revision History  

• Version 1.0: 2023-03-22
  Type: Initial release
  
• Version 1.1: 2023-04-19
  Changes: Database references
• Version 1.2: 2024-02-14
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.3: 2025-07-02
  Changes: Data collection, Structure summary
• Version 1.4: 2025-10-01
  Changes: Advisory, Data collection, Derived calculations