9UI4 | pdb_00009ui4

Rad51 presynaptic complex

PDB DOI: https://doi.org/10.2210/pdb9UI4/pdb
EM Map EMD-64183: EMDB EMDataResource
NAKB: 9UI4

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: 2.91 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 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: 368.94 kDa
Atom Count: 22,055
Modeled Residue Count: 2,783
Deposited Residue Count: 3,276
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein RAD51 homolog 1	B [auth C] C [auth B] D [auth A] E [auth F] F [auth I] B [auth C], C [auth B], D [auth A], E [auth F], F [auth I], G [auth E], H, I [auth D], J [auth G]	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

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	A [auth L]	27	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 AA [auth G] SDF format, chain K [auth C] SDF format, chain M [auth B] SDF format, chain O [auth A] SDF format, chain R [auth I] SDF format, chain T [auth E] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth G] MOL2 format, chain AA [auth G] MOL2 format, chain K [auth C] MOL2 format, chain M [auth B] MOL2 format, chain O [auth A] MOL2 format, chain R [auth I] MOL2 format, chain T [auth E] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth G] mmCIF format, chain AA [auth G] mmCIF format, chain K [auth C] mmCIF format, chain M [auth B] mmCIF format, chain O [auth A] mmCIF format, chain R [auth I] mmCIF format, chain T [auth E] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth G]	AA [auth G] K [auth C] M [auth B] O [auth A] R [auth I] AA [auth G], K [auth C], M [auth B], O [auth A], R [auth I], T [auth E], W [auth D], X [auth D], Z [auth G]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain AA [auth G] Focus chain K [auth C] Focus chain M [auth B] Focus chain O [auth A] Focus chain R [auth I] Focus chain T [auth E] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth G] Interactions & Density Focus chain AA [auth G] Focus chain K [auth C] Focus chain M [auth B] Focus chain O [auth A] Focus chain R [auth I] Focus chain T [auth E] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain L [auth C] SDF format, chain N [auth B] SDF format, chain P [auth A] SDF format, chain Q [auth F] SDF format, chain S [auth I] SDF format, chain U [auth E] SDF format, chain V [auth H] SDF format, chain Y [auth D] MOL2 format, chain BA [auth G] MOL2 format, chain L [auth C] MOL2 format, chain N [auth B] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth F] MOL2 format, chain S [auth I] MOL2 format, chain U [auth E] MOL2 format, chain V [auth H] MOL2 format, chain Y [auth D] mmCIF format, chain BA [auth G] mmCIF format, chain L [auth C] mmCIF format, chain N [auth B] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth F] mmCIF format, chain S [auth I] mmCIF format, chain U [auth E] mmCIF format, chain V [auth H] mmCIF format, chain Y [auth D]	BA [auth G] L [auth C] N [auth B] P [auth A] Q [auth F] BA [auth G], L [auth C], N [auth B], P [auth A], Q [auth F], S [auth I], U [auth E], V [auth H], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth A] Focus chain Q [auth F] Focus chain S [auth I] Focus chain U [auth E] Focus chain V [auth H] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth G] Focus chain L [auth C] Focus chain N [auth B] Focus chain P [auth A] Focus chain Q [auth F] Focus chain S [auth I] Focus chain U [auth E] Focus chain V [auth H] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.91 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419:
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Luo, S.C.

Ho, M.C.

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	AS-TP-113-L01 to M.C.H

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release
Version 2.0: 2025-11-05
Type: Coordinate replacement
Reason: Polymer geometry
Changes: Advisory, Atomic model, Data collection, Derived calculations, Refinement description, Structure summary