23WQ | pdb_000023wq

Cryo-EM structure of EcBPAN-guide RNA-target DNA complex

PDB DOI: https://doi.org/10.2210/pdb23WQ/pdb
EM Map EMD-69324: EMDB EMDataResource

Classification: DNA BINDING PROTEIN/DNA/RNA
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2026-02-23 Released: 2026-08-26
Deposition Author(s): Liu, M., Yu, Q., Shi, D.J., Xing, Q., Ma, L.X.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of EcBPAN-guide RNA-target DNA complex

Liu, M., Yu, Q., Shi, D.J., Xing, Q., Ma, L.X.

To be published.

Macromolecule Content

Total Structure Weight: 1,121 kDa
Atom Count: 77,641
Modeled Residue Count: 9,237
Deposited Residue Count: 9,304
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
EcbAgaN	C [auth 1] D [auth 2] E [auth 4] EA [auth 5] F [auth 3] C [auth 1], D [auth 2], E [auth 4], EA [auth 5], F [auth 3], FA [auth 6], G [auth 8], H [auth 7]	390	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
EcAgo	AA [auth a] BA [auth b] CA [auth c] DA [auth d] I [auth f] AA [auth a], BA [auth b], CA [auth c], DA [auth d], I [auth f], J [auth e], S [auth g], X [auth h]	731	Escherichia coli	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
RNA (5'-R(PAPUPCPAPAPAPGPCPUPUPAPGPAPUPAPCPCPCPUPGP*G)-3')	A K [auth C] M [auth E] P [auth H] Q [auth K] A, K [auth C], M [auth E], P [auth H], Q [auth K], U [auth N], V [auth O], Y [auth I]	21	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 2
DNA (5'-D(CPCPAPGPGPGPTPAPTPCPTPAPAPGPCPTPTPTPGPAP*T)-3')	B L [auth D] N [auth F] O [auth G] R [auth L] B, L [auth D], N [auth F], O [auth G], R [auth L], T [auth M], W [auth P], Z [auth J]	21	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain HA [auth C] SDF format, chain JA [auth H] SDF format, chain KA [auth K] SDF format, chain LA [auth N] SDF format, chain MA [auth O] SDF format, chain NA [auth I] SDF format, chain IA [auth E] MOL2 format, chain GA [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain JA [auth H] MOL2 format, chain KA [auth K] MOL2 format, chain LA [auth N] MOL2 format, chain MA [auth O] MOL2 format, chain NA [auth I] MOL2 format, chain IA [auth E] mmCIF format, chain GA [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain JA [auth H] mmCIF format, chain KA [auth K] mmCIF format, chain LA [auth N] mmCIF format, chain MA [auth O] mmCIF format, chain NA [auth I] mmCIF format, chain IA [auth E]	GA [auth A] HA [auth C] IA [auth E] JA [auth H] KA [auth K] GA [auth A], HA [auth C], IA [auth E], JA [auth H], KA [auth K], LA [auth N], MA [auth O], NA [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Focus chain HA [auth C] Focus chain IA [auth E] Focus chain JA [auth H] Focus chain KA [auth K] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth I] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth C] Focus chain IA [auth E] Focus chain JA [auth H] Focus chain KA [auth K] Focus chain LA [auth N] Focus chain MA [auth O] Focus chain NA [auth I]