9QN8 | pdb_00009qn8

RAD51 filament in complex with calcium and ATP bound by the RAD51AP1 C-terminus

PDB DOI: https://doi.org/10.2210/pdb9QN8/pdb
EM Map EMD-53239: 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: 3.14 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

RAD51AP1 is a versatile RAD51 modulator

Kuhlen, L., Zhang, X.

To be published.

Macromolecule Content

Total Structure Weight: 471.85 kDa
Atom Count: 15,950
Modeled Residue Count: 2,025
Deposited Residue Count: 4,239
Unique protein chains: 2
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, C, E, G, I A, C, E, G, I, 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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RAD51-associated protein 1	B, D, F, H, J B, D, F, H, J, L	364	Homo sapiens	Mutation(s): 0 Gene Names: RAD51AP1, PIR51
UniProt & NIH Common Fund Data Resources
Find proteins for Q96B01 (Homo sapiens) Explore Q96B01 Go to UniProtKB: Q96B01
PHAROS: Q96B01 GTEx: ENSG00000111247
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96B01
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA	M [auth Z]	21	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 R [auth C] SDF format, chain U [auth E] SDF format, chain X [auth G] SDF format, chain N [auth A] SDF format, chain EA [auth K] SDF format, chain DA [auth K] SDF format, chain AA [auth I] MOL2 format, chain R [auth C] MOL2 format, chain U [auth E] MOL2 format, chain X [auth G] MOL2 format, chain N [auth A] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth K] MOL2 format, chain AA [auth I] mmCIF format, chain R [auth C] mmCIF format, chain U [auth E] mmCIF format, chain X [auth G] mmCIF format, chain N [auth A] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth K] mmCIF format, chain AA [auth I]	AA [auth I] DA [auth K] EA [auth K] N [auth A] R [auth C] AA [auth I], DA [auth K], EA [auth K], N [auth A], R [auth C], U [auth E], X [auth G]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AA [auth I] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain N [auth A] Focus chain R [auth C] Focus chain U [auth E] Focus chain X [auth G] Interactions & Density Focus chain AA [auth I] Focus chain DA [auth K] Focus chain EA [auth K] Focus chain N [auth A] Focus chain R [auth C] Focus chain U [auth E] Focus chain X [auth G]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain FA [auth K] SDF format, chain GA [auth K] SDF format, chain V [auth E] SDF format, chain Y [auth G] SDF format, chain S [auth C] SDF format, chain O [auth A] SDF format, chain BA [auth I] MOL2 format, chain FA [auth K] MOL2 format, chain GA [auth K] MOL2 format, chain V [auth E] MOL2 format, chain Y [auth G] MOL2 format, chain S [auth C] MOL2 format, chain O [auth A] MOL2 format, chain BA [auth I] mmCIF format, chain FA [auth K] mmCIF format, chain GA [auth K] mmCIF format, chain V [auth E] mmCIF format, chain Y [auth G] mmCIF format, chain S [auth C] mmCIF format, chain O [auth A] mmCIF format, chain BA [auth I]	BA [auth I] FA [auth K] GA [auth K] O [auth A] S [auth C] BA [auth I], FA [auth K], GA [auth K], O [auth A], S [auth C], V [auth E], Y [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain O [auth A] Focus chain S [auth C] Focus chain V [auth E] Focus chain Y [auth G] Interactions & Density Focus chain BA [auth I] Focus chain FA [auth K] Focus chain GA [auth K] Focus chain O [auth A] Focus chain S [auth C] Focus chain V [auth E] Focus chain Y [auth G]
K (Subject of Investigation/LOI) Query on K Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain HA [auth K] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain T [auth C] SDF format, chain W [auth E] SDF format, chain Z [auth G] MOL2 format, chain CA [auth I] MOL2 format, chain HA [auth K] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth C] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth G] mmCIF format, chain CA [auth I] mmCIF format, chain HA [auth K] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain T [auth C] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth G]	CA [auth I] HA [auth K] P [auth A] Q [auth A] T [auth C] CA [auth I], HA [auth K], P [auth A], Q [auth A], T [auth C], W [auth E], Z [auth G]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain CA [auth I] Focus chain HA [auth K] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth C] Focus chain W [auth E] Focus chain Z [auth G] Interactions & Density Focus chain CA [auth I] Focus chain HA [auth K] Focus chain P [auth A] Focus chain Q [auth A] Focus chain T [auth C] Focus chain W [auth E] Focus chain Z [auth G]