9D4N | pdb_00009d4n

The cryo-EM structure of the yeast Dmc1 filament bound to ssDNA in the presence of ATP

PDB DOI: https://doi.org/10.2210/pdb9D4N/pdb
EM Map EMD-46565: EMDB EMDataResource
NAKB: 9D4N

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

Deposited: 2024-08-12 Released: 2025-01-22
Deposition Author(s): Shin, Y., Greene, E.C.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

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

Shin, Y., Greene, E.C.

To be published.

Macromolecule Content

Total Structure Weight: 228.71 kDa
Atom Count: 14,952
Modeled Residue Count: 1,884
Deposited Residue Count: 2,022
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Meiotic recombination protein DMC1	A, B, C, D, E A, B, C, D, E, F	334	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: DMC1, ISC2, YER179W
UniProt
Find proteins for P25453 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25453 Go to UniProtKB: P25453
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25453
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPTPT)-3')	G [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 V [auth F] SDF format, chain S [auth E] SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain V [auth F] MOL2 format, chain S [auth E] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain V [auth F] mmCIF format, chain S [auth E] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] M [auth C] P [auth D] S [auth E] H [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain X [auth F] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth A] MOL2 format, chain Y [auth F] MOL2 format, chain X [auth F] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth F] mmCIF format, chain X [auth F] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth A]	I [auth A] K [auth B] L [auth B] N [auth C] O [auth C] I [auth A], K [auth B], L [auth B], N [auth C], O [auth C], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F], X [auth F], Y [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Focus chain X [auth F] Focus chain Y [auth F]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-22

Deposition Author(s):

Shin, Y.

Greene, E.C.

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-MCB1817315

Revision History (Full details and data files)

Version 1.0: 2025-01-22
Type: Initial release
Version 2.0: 2025-02-19
Type: Coordinate replacement
Reason: Atomic clashes
Changes: Atomic model, Data collection, Data processing, Derived calculations, Structure summary