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- PDB-9wmh: Cryo-EM strucutre of MbpAgo-gDNA-tgRNA complex -

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Basic information

Entry
Database: PDB / ID: 9wmh
TitleCryo-EM strucutre of MbpAgo-gDNA-tgRNA complex
Components
  • Guide DNA
  • Piwi domain-containing protein
  • Target RNA
KeywordsRNA BINDING PROTEIN/DNA/RNA / Mucilaginibacter paludis Argonaute with guide DNA / RNA BINDING PROTEIN-DNA-RNA complex
Function / homologyRibonuclease H superfamily / nucleic acid binding / Ribonuclease H-like superfamily / DNA / DNA (> 10) / RNA / RNA (> 10) / Piwi domain-containing protein
Function and homology information
Biological speciesMucilaginibacter paludis DSM 18603 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsZhao, X. / Zhang, K. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural and mechanistic insights into MbpAgo
Authors: Zhao, X. / Zhang, K. / Li, S.
History
DepositionSep 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 13, 2026Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 13, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Piwi domain-containing protein
B: Guide DNA
C: Target RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5166
Polymers105,3963
Non-polymers1203
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: Protein Piwi domain-containing protein / Argonaute


Mass: 93827.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mucilaginibacter paludis DSM 18603 (bacteria)
Gene: Mucpa_0938 / Production host: Escherichia coli (E. coli) / References: UniProt: H1YCU5
#2: DNA chain Guide DNA


Mass: 5641.660 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain Target RNA


Mass: 5926.584 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / 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: MbpAgo-gDNA-tgRNA complex / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Mucilaginibacter paludis
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenConc.: 0.46 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 52.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
9PHENIXmodel refinement
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1175425 / Symmetry type: POINT

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