9UI5 | pdb_00009ui5

Rad51 postsynaptic complex

PDB DOI: https://doi.org/10.2210/pdb9UI5/pdb
EM Map EMD-64184: EMDB EMDataResource
NAKB: 9UI5

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

Deposited: 2025-04-15 Released: 2025-09-17
Deposition Author(s): Luo, S.C., Ho, M.C.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.04 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: 377.39 kDa
Atom Count: 22,849
Modeled Residue Count: 2,856
Deposited Residue Count: 3,303
Unique protein chains: 1
Unique nucleic acid chains: 2

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] D [auth H] E [auth I] A [auth E], B [auth F], C [auth G], D [auth H], E [auth I], H [auth A], I [auth B], J [auth C], K [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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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (27-MER)	F [auth L]	27	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 (27-MER)	G [auth M]	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 Z [auth C] SDF format, chain X [auth B] SDF format, chain V [auth A] SDF format, chain T [auth H] SDF format, chain R [auth G] SDF format, chain P [auth G] SDF format, chain N [auth F] SDF format, chain L [auth E] SDF format, chain BA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain X [auth B] MOL2 format, chain V [auth A] MOL2 format, chain T [auth H] MOL2 format, chain R [auth G] MOL2 format, chain P [auth G] MOL2 format, chain N [auth F] MOL2 format, chain L [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain X [auth B] mmCIF format, chain V [auth A] mmCIF format, chain T [auth H] mmCIF format, chain R [auth G] mmCIF format, chain P [auth G] mmCIF format, chain N [auth F] mmCIF format, chain L [auth E] mmCIF format, chain BA [auth D]	BA [auth D] L [auth E] N [auth F] P [auth G] R [auth G] BA [auth D], L [auth E], N [auth F], P [auth G], R [auth G], T [auth H], V [auth A], X [auth B], Z [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain BA [auth D] Focus chain L [auth E] Focus chain N [auth F] Focus chain P [auth G] Focus chain R [auth G] Focus chain T [auth H] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C] Interactions & Density Focus chain BA [auth D] Focus chain L [auth E] Focus chain N [auth F] Focus chain P [auth G] Focus chain R [auth G] Focus chain T [auth H] Focus chain V [auth A] Focus chain X [auth B] Focus chain Z [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain W [auth A] SDF format, chain U [auth H] 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 H] 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 H] 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 H], W [auth A], Y [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-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 H] 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 H] Focus chain W [auth A] Focus chain Y [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.04 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: 2025-09-17

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: 2025-09-17
Type: Initial release
Version 1.1: 2025-10-01
Changes: Data collection, Data processing
Version 2.0: 2025-11-05
Type: Coordinate replacement
Reason: Model orientation/position
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Refinement description, Source and taxonomy, Structure summary