8GYK | pdb_00008gyk

CryoEM structure of the RAD51_ADP filament

PDB DOI: https://doi.org/10.2210/pdb8GYK/pdb
EM Map EMD-34372: EMDB EMDataResource

Classification: RECOMBINATION
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-09-22 Released: 2023-08-30
Deposition Author(s): Miki, Y., Luo, S.C., Ho, M.C.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.14 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

A RAD51-ADP double filament structure unveils the mechanism of filament dynamics in homologous recombination.

Luo, S.C., Yeh, M.C., Lien, Y.H., Yeh, H.Y., Siao, H.L., Tu, I.P., Chi, P., Ho, M.C.

(2023) Nat Commun 14: 4993-4993

PubMed: 37591853 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-023-40672-5
Primary Citation Related Structures:
8GYK

PubMed Abstract:
ATP-dependent RAD51 recombinases play an essential role in eukaryotic homologous recombination by catalyzing a four-step process: 1) formation of a RAD51 single-filament assembly on ssDNA in the presence of ATP, 2) complementary DNA strand-exchange, 3) ATP hydrolysis transforming the RAD51 filament into an ADP-bound disassembly-competent state, and 4) RAD51 disassembly to provide access for DNA repairing enzymes. Of these steps, filament dynamics between the ATP- and ADP-bound states, and the RAD51 disassembly mechanism, are poorly understood due to the lack of near-atomic-resolution information of the ADP-bound RAD51-DNA filament structure. We report the cryo-EM structure of ADP-bound RAD51-DNA filaments at 3.1 Å resolution, revealing a unique RAD51 double-filament that wraps around ssDNA. Structural analysis, supported by ATP-chase and time-resolved cryo-EM experiments, reveals a collapsing mechanism involving two four-protomer movements along ssDNA for mechanical transition between RAD51 single- and double-filament without RAD51 dissociation. This mechanism enables elastic change of RAD51 filament length during structural transitions between ATP- and ADP-states.

Organizational Affiliation

Institute of Biological Chemistry, Academia Sinica, 11529, Taipei, Taiwan.

Macromolecule Content

Total Structure Weight: 299.69 kDa
Atom Count: 18,103
Modeled Residue Count: 2,325
Deposited Residue Count: 2,712
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	A, B, C, D, E A, B, C, D, E, F, G, H	339	Homo sapiens	Mutation(s): 0 Gene Names: RAD51, RAD51A, RECA EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q06609 (Homo sapiens) Explore Q06609 Go to UniProtKB: Q06609
PHAROS: Q06609 GTEx: ENSG00000051180
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q06609
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain U [auth G] SDF format, chain W [auth H] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain U [auth G] MOL2 format, chain W [auth H] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain U [auth G] mmCIF format, chain W [auth H]	I [auth A] K [auth B] M [auth C] O [auth D] Q [auth E] I [auth A], K [auth B], M [auth C], O [auth D], Q [auth E], S [auth F], U [auth G], W [auth H]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain M [auth C] Focus chain O [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain U [auth G] Focus chain W [auth H]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain L [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain V [auth G] SDF format, chain X [auth H] MOL2 format, chain J [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain V [auth G] MOL2 format, chain X [auth H] mmCIF format, chain J [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain V [auth G] mmCIF format, chain X [auth H]	J [auth A] L [auth B] N [auth C] P [auth D] R [auth E] J [auth A], L [auth B], N [auth C], P [auth D], R [auth E], T [auth F], V [auth G], X [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H] Interactions & Density Focus chain J [auth A] Focus chain L [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain R [auth E] Focus chain T [auth F] Focus chain V [auth G] Focus chain X [auth H]