9UI9 | pdb_00009ui9

structure of a 12 base pair Rad51 D-loop complex

PDB DOI: https://doi.org/10.2210/pdb9UI9/pdb
EM Map EMD-64188: EMDB EMDataResource
NAKB: 9UI9

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-04-15 Released: 2025-09-10
Deposition Author(s): Luo, S.C., Ho, M.C.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.42 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

Mechanism of strand exchange of eukaryotic homologous recombination from RAD51 D-loop structures

Luo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 400.95 kDa
Atom Count: 23,613
Modeled Residue Count: 2,894
Deposited Residue Count: 3,380
Unique protein chains: 1
Unique nucleic acid chains: 3

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 [auth E] B [auth F] C [auth G] F [auth H] G [auth I] A [auth E], B [auth F], C [auth G], F [auth H], G [auth I], I [auth A], J [auth B], K [auth C], L [auth D]	361	Mus musculus	Mutation(s): 2 Gene Names: Rad51, Rad51a, Reca
UniProt
Find proteins for Q08297 (Mus musculus) Explore Q08297 Go to UniProtKB: Q08297
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q08297
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	D [auth U]	48	Mus musculus
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (48-MER)	E [auth T]	48	Mus musculus
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (35-MER)	H [auth L]	35	Mus musculus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain W [auth A] SDF format, chain U [auth I] SDF format, chain S [auth H] SDF format, chain Q [auth G] SDF format, chain O [auth F] SDF format, chain M [auth E] SDF format, chain CA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth A] MOL2 format, chain U [auth I] MOL2 format, chain S [auth H] MOL2 format, chain Q [auth G] MOL2 format, chain O [auth F] MOL2 format, chain M [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth A] mmCIF format, chain U [auth I] mmCIF format, chain S [auth H] mmCIF format, chain Q [auth G] mmCIF format, chain O [auth F] mmCIF format, chain M [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] CA [auth D] M [auth E] O [auth F] Q [auth G] AA [auth C], CA [auth D], M [auth E], O [auth F], Q [auth G], S [auth H], U [auth I], W [auth A], Y [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain M [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth D] Focus chain M [auth E] Focus chain O [auth F] Focus chain Q [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain W [auth A] Focus chain Y [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain X [auth A] SDF format, chain V [auth I] SDF format, chain T [auth H] SDF format, chain R [auth G] SDF format, chain P [auth F] SDF format, chain N [auth E] SDF format, chain DA [auth D] SDF format, chain BA [auth C] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth A] MOL2 format, chain V [auth I] MOL2 format, chain T [auth H] MOL2 format, chain R [auth G] MOL2 format, chain P [auth F] MOL2 format, chain N [auth E] MOL2 format, chain DA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth A] mmCIF format, chain V [auth I] mmCIF format, chain T [auth H] mmCIF format, chain R [auth G] mmCIF format, chain P [auth F] mmCIF format, chain N [auth E] mmCIF format, chain DA [auth D] mmCIF format, chain BA [auth C]	BA [auth C] DA [auth D] N [auth E] P [auth F] R [auth G] BA [auth C], DA [auth D], N [auth E], P [auth F], R [auth G], T [auth H], V [auth I], X [auth A], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain DA [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain T [auth H] Focus chain V [auth I] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth D] Focus chain N [auth E] Focus chain P [auth F] Focus chain R [auth G] Focus chain T [auth H] Focus chain V [auth I] Focus chain X [auth A] Focus chain Z [auth B]