9I62 | pdb_00009i62

CryoEM structure of a RAD51 D-loop

PDB DOI: https://doi.org/10.2210/pdb9I62/pdb
EM Map EMD-52646: EMDB EMDataResource
NAKB: 9I62

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-01-29 Released: 2025-06-04
Deposition Author(s): Pellegrini, L., Joudeh, L., Appleby, R.E.
Funding Organization(s): Wellcome Trust, UK Research and Innovation (UKRI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.64 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

Structural mechanism of strand exchange by the RAD51 filament.

Joudeh, L., Appleby, R.E., Maman, J.D., Pellegrini, L.

(2025) Elife 14

PubMed: 40820711 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.7554/eLife.107114
Primary Citation Related Structures:
9I62

PubMed Abstract:
Homologous recombination (HR) preserves genomic stability by repairing double-strand DNA breaks and ensuring efficient DNA replication. Central to HR is the strand-exchange reaction taking place within the three-stranded synapsis wherein a RAD51 nucleoprotein filament binds to a donor DNA. Here, we present the cryoEM structure of a displacement loop of human RAD51 that captures the synaptic state when the filament has become tightly bound to the donor DNA. The structure elucidates the mechanism of strand exchange by RAD51, including the filament engagement with the donor DNA, the strand invasion and pairing with the complementary sequence of the donor DNA, the capture of the non-complementary strand and the polarity of the strand-exchange reaction. Our findings provide fundamental mechanistic insights into the biochemical reaction of eukaryotic HR.

Organizational Affiliation

Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

Macromolecule Content

Total Structure Weight: 378.88 kDa
Atom Count: 24,205
Modeled Residue Count: 2,939
Deposited Residue Count: 3,183
Unique protein chains: 1
Unique nucleic acid chains: 3

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, I	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

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (26-MER)	J	32	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 3
DNA (41-MER)	K	50	synthetic construct
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 4
DNA (41-MER)	L	50	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain JA [auth H] SDF format, chain MA [auth I] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D] mmCIF format, chain AA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain GA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain MA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth D]	AA [auth E] DA [auth F] GA [auth G] JA [auth H] MA [auth I] AA [auth E], DA [auth F], GA [auth G], JA [auth H], MA [auth I], O [auth A], R [auth B], U [auth C], X [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain HA [auth H] SDF format, chain IA [auth H] SDF format, chain KA [auth I] SDF format, chain LA [auth I] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E]	BA [auth F] CA [auth F] EA [auth G] FA [auth G] HA [auth H] BA [auth F], CA [auth F], EA [auth G], FA [auth G], HA [auth H], IA [auth H], KA [auth I], LA [auth I], M [auth A], N [auth A], P [auth B], Q [auth B], S [auth C], T [auth C], V [auth D], W [auth D], Y [auth E], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain KA [auth I] Focus chain LA [auth I] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]