9NJK | pdb_00009njk

The Cryo-EM structure of the yeast Rad51-ssDNA nucleoprotein filament ADP bound state

PDB DOI: https://doi.org/10.2210/pdb9NJK/pdb
EM Map EMD-49485: EMDB EMDataResource

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

Deposited: 2025-02-27 Released: 2025-03-19
Deposition Author(s): Shin, Y., Greene, E.C.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.37 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

The Cryo-EM structure of the yeast Rad51-ssDNA nucleoprotein filament ADP bound state

Shin, Y., Greene, E.C.

To be published.

Macromolecule Content

Total Structure Weight: 259.85 kDa
Atom Count: 13,780
Modelled Residue Count: 1,789
Deposited Residue Count: 2,400
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51	A [auth D] B [auth C] C [auth E] D [auth F] E [auth B] A [auth D], B [auth C], C [auth E], D [auth F], E [auth B], F [auth A]	400	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain I [auth C] SDF format, chain K [auth B] SDF format, chain M [auth A] MOL2 format, chain G [auth D] MOL2 format, chain I [auth C] MOL2 format, chain K [auth B] MOL2 format, chain M [auth A] mmCIF format, chain G [auth D] mmCIF format, chain I [auth C] mmCIF format, chain K [auth B] mmCIF format, chain M [auth A]	G [auth D], I [auth C], K [auth B], M [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain G [auth D] Focus chain I [auth C] Focus chain K [auth B] Focus chain M [auth A] Interactions & Density Focus chain G [auth D] Focus chain I [auth C] Focus chain K [auth B] Focus chain M [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain J [auth C] SDF format, chain L [auth B] SDF format, chain N [auth A] MOL2 format, chain H [auth D] MOL2 format, chain J [auth C] MOL2 format, chain L [auth B] MOL2 format, chain N [auth A] mmCIF format, chain H [auth D] mmCIF format, chain J [auth C] mmCIF format, chain L [auth B] mmCIF format, chain N [auth A]	H [auth D], J [auth C], L [auth B], N [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth D] Focus chain J [auth C] Focus chain L [auth B] Focus chain N [auth A] Interactions & Density Focus chain H [auth D] Focus chain J [auth C] Focus chain L [auth B] Focus chain N [auth A]