9QNA | pdb_00009qna

RAD51 filament in complex with magnesium and ATP

PDB DOI: https://doi.org/10.2210/pdb9QNA/pdb
EM Map EMD-53241: EMDB EMDataResource

Classification: DNA BINDING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-03-24 Released: 2025-12-03
Deposition Author(s): Kuhlen, L., Zhang, X.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.26 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

RAD51AP1 is a versatile RAD51 modulator

Kuhlen, L., Zhang, X.

To be published.

Macromolecule Content

Total Structure Weight: 244.25 kDa
Atom Count: 14,931
Modeled Residue Count: 1,885
Deposited Residue Count: 2,094
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	A B [auth C] C [auth E] D [auth G] E [auth I] A, B [auth C], C [auth E], D [auth G], E [auth I], F [auth K]	339	Homo sapiens	Mutation(s): 0 Gene Names: RAD51, RAD51A, RECA
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q06609
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	G [auth Z]	60	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 H [auth A] SDF format, chain K [auth C] SDF format, chain N [auth E] SDF format, chain Q [auth G] SDF format, chain T [auth I] SDF format, chain W [auth K] SDF format, chain X [auth K] MOL2 format, chain H [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth E] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth I] MOL2 format, chain W [auth K] MOL2 format, chain X [auth K] mmCIF format, chain H [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth E] mmCIF format, chain Q [auth G] mmCIF format, chain T [auth I] mmCIF format, chain W [auth K] mmCIF format, chain X [auth K]	H [auth A] K [auth C] N [auth E] Q [auth G] T [auth I] H [auth A], K [auth C], N [auth E], Q [auth G], T [auth I], W [auth K], X [auth K]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth E] Focus chain Q [auth G] Focus chain T [auth I] Focus chain W [auth K] Focus chain X [auth K] Interactions & Density Focus chain H [auth A] Focus chain K [auth C] Focus chain N [auth E] Focus chain Q [auth G] Focus chain T [auth I] Focus chain W [auth K] Focus chain X [auth K]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth C] SDF format, chain P [auth E] SDF format, chain S [auth G] SDF format, chain V [auth I] SDF format, chain Z [auth K] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain P [auth E] MOL2 format, chain S [auth G] MOL2 format, chain V [auth I] MOL2 format, chain Z [auth K] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain P [auth E] mmCIF format, chain S [auth G] mmCIF format, chain V [auth I] mmCIF format, chain Z [auth K]	J [auth A] M [auth C] P [auth E] S [auth G] V [auth I] J [auth A], M [auth C], P [auth E], S [auth G], V [auth I], Z [auth K]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth G] Focus chain V [auth I] Focus chain Z [auth K] Interactions & Density Focus chain J [auth A] Focus chain M [auth C] Focus chain P [auth E] Focus chain S [auth G] Focus chain V [auth I] Focus chain Z [auth K]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain O [auth E] SDF format, chain R [auth G] SDF format, chain U [auth I] SDF format, chain Y [auth K] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain O [auth E] MOL2 format, chain R [auth G] MOL2 format, chain U [auth I] MOL2 format, chain Y [auth K] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain O [auth E] mmCIF format, chain R [auth G] mmCIF format, chain U [auth I] mmCIF format, chain Y [auth K]	I [auth A] L [auth C] O [auth E] R [auth G] U [auth I] I [auth A], L [auth C], O [auth E], R [auth G], U [auth I], Y [auth K]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G] Focus chain U [auth I] Focus chain Y [auth K] Interactions & Density Focus chain I [auth A] Focus chain L [auth C] Focus chain O [auth E] Focus chain R [auth G] Focus chain U [auth I] Focus chain Y [auth K]