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- PDB-9nnk: Cryo-EM structure of Retron-displaced free PtuAB complex, PtuA:Pt... -

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Basic information

Entry
Database: PDB / ID: 9nnk
TitleCryo-EM structure of Retron-displaced free PtuAB complex, PtuA:PtuB (4:2)
Components
  • Retreon I-A effector PtuA
  • Retron I-A effector PtuB
KeywordsTOXIN / Retron effector / ATPase / HNH nuclease
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Retron Ec78 probable ATPase / Retron Ec78 putative HNH endonuclease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsWang, B. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 United States
CitationJournal: To Be Published
Title: Structure Basis for Retron Co-option of Anti-phage ATPase-nuclease
Authors: Wang, B. / Hou, Y.M. / Li, H.
History
DepositionMar 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 8, 2025Data 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
C: Retreon I-A effector PtuA
D: Retreon I-A effector PtuA
J: Retron I-A effector PtuB
E: Retreon I-A effector PtuA
F: Retreon I-A effector PtuA
K: Retron I-A effector PtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)301,76810
Polymers299,7396
Non-polymers2,0294
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Retreon I-A effector PtuA


Mass: 62451.805 Da / Num. of mol.: 4 / Mutation: Q361L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0100609_101823 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DV91
#2: Protein Retron I-A effector PtuB / TIGR02646 family protein


Mass: 24966.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Ga0100609_101824 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DV92
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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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: Retron-displaced free PtuAB complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: 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: OTHER / Nominal defocus max: 1700 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
13PHENIX1.20.1_4487model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 281151 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.07 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.006921472
ELECTRON MICROSCOPYf_angle_d1.074228992
ELECTRON MICROSCOPYf_chiral_restr0.05833200
ELECTRON MICROSCOPYf_plane_restr0.00683760
ELECTRON MICROSCOPYf_dihedral_angle_d6.32262848

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