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- PDB-23wq: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex -

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Basic information

Entry
Database: PDB / ID: 23wq
TitleCryo-EM structure of EcBPAN-guide RNA-target DNA complex
Components
  • DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
  • EcAgo
  • EcbAgaN
  • RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
KeywordsDNA BINDING PROTEIN/DNA/RNA / Argonaute proteins / nucleic acid binding / nuclease / defence system / DNA BINDING PROTEIN-DNA-RNA complex
Function / homologyDNA / DNA (> 10) / RNA / RNA (> 10)
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsLiu, M. / Yu, Q. / Shi, D.J. / Xing, Q. / Ma, L.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
Authors: Liu, M. / Yu, Q. / Shi, D.J. / Xing, Q. / Ma, L.X.
History
DepositionFeb 23, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
B: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
1: EcbAgaN
2: EcbAgaN
4: EcbAgaN
3: EcbAgaN
8: EcbAgaN
7: EcbAgaN
f: EcAgo
e: EcAgo
C: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
D: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
E: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
F: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
G: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
H: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
K: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
L: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
g: EcAgo
M: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
N: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
O: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
P: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
h: EcAgo
I: RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')
J: DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')
a: EcAgo
b: EcAgo
c: EcAgo
d: EcAgo
5: EcbAgaN
6: EcbAgaN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,120,99540
Polymers1,120,80132
Non-polymers1948
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain
RNA (5'-R(P*AP*UP*CP*AP*AP*AP*GP*CP*UP*UP*AP*GP*AP*UP*AP*CP*CP*CP*UP*GP*G)-3')


Mass: 6697.044 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: DNA chain
DNA (5'-D(*CP*CP*AP*GP*GP*GP*TP*AP*TP*CP*TP*AP*AP*GP*CP*TP*TP*TP*GP*AP*T)-3')


Mass: 6453.182 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Protein
EcbAgaN


Mass: 44457.730 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Protein
EcAgo


Mass: 82492.133 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of EcBPAN-guide RNA-target DNA complex
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13Coot3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309746 / Symmetry type: POINT
RefinementHighest resolution: 3.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00579987
ELECTRON MICROSCOPYf_angle_d0.482109593
ELECTRON MICROSCOPYf_dihedral_angle_d14.54113504
ELECTRON MICROSCOPYf_chiral_restr0.04212282
ELECTRON MICROSCOPYf_plane_restr0.00412922

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