9D46 | pdb_00009d46

The cryo-EM structure of the yeast RAD51 filament bound to ssDNA in the presence of ATP

PDB DOI: https://doi.org/10.2210/pdb9D46/pdb
EM Map EMD-46550: EMDB EMDataResource
NAKB: 9D46

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Saccharomyces cerevisiae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-08-12 Released: 2025-02-19
Deposition Author(s): Shin, Y., Greene, E.C.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.06 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases

Petassi, M., Shin, Y., Jessop, A.M., Morse, K., Kim, S.Y., Kuppa, S., Matei, R., Raina, V.B., Greene, E.C.

(2026) J Biological Chem 302

DOI: https://doi.org/10.1016/j.jbc.2025.111019

Macromolecule Content

Total Structure Weight: 218.35 kDa
Atom Count: 15,188
Modeled Residue Count: 1,942
Deposited Residue Count: 1,944
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51	B [auth C] C [auth F] D [auth B] E F [auth A] B [auth C], C [auth F], D [auth B], E, F [auth A], G [auth D]	321	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RAD51, YER095W
UniProt
Find proteins for P25454 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25454 Go to UniProtKB: P25454
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25454
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	A [auth X]	18	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain K [auth F] SDF format, chain O [auth B] SDF format, chain R [auth E] SDF format, chain U [auth A] SDF format, chain W [auth D] MOL2 format, chain H [auth C] MOL2 format, chain K [auth F] MOL2 format, chain O [auth B] MOL2 format, chain R [auth E] MOL2 format, chain U [auth A] MOL2 format, chain W [auth D] mmCIF format, chain H [auth C] mmCIF format, chain K [auth F] mmCIF format, chain O [auth B] mmCIF format, chain R [auth E] mmCIF format, chain U [auth A] mmCIF format, chain W [auth D]	H [auth C] K [auth F] O [auth B] R [auth E] U [auth A] H [auth C], K [auth F], O [auth B], R [auth E], U [auth A], W [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth C] Focus chain K [auth F] Focus chain O [auth B] Focus chain R [auth E] Focus chain U [auth A] Focus chain W [auth D] Interactions & Density Focus chain H [auth C] Focus chain K [auth F] Focus chain O [auth B] Focus chain R [auth E] Focus chain U [auth A] Focus chain W [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain J [auth C] SDF format, chain L [auth F] SDF format, chain M [auth F] SDF format, chain N [auth F] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain V [auth A] SDF format, chain Y [auth D] SDF format, chain X [auth D] MOL2 format, chain I [auth C] MOL2 format, chain J [auth C] MOL2 format, chain L [auth F] MOL2 format, chain M [auth F] MOL2 format, chain N [auth F] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] mmCIF format, chain I [auth C] mmCIF format, chain J [auth C] mmCIF format, chain L [auth F] mmCIF format, chain M [auth F] mmCIF format, chain N [auth F] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D]	I [auth C] J [auth C] L [auth F] M [auth F] N [auth F] I [auth C], J [auth C], L [auth F], M [auth F], N [auth F], P [auth B], Q [auth B], S [auth E], T [auth E], V [auth A], X [auth D], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth A] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth F] Focus chain M [auth F] Focus chain N [auth F] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth E] Focus chain T [auth E] Focus chain V [auth A] Focus chain X [auth D] Focus chain Y [auth D]