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- PDB-9nnb: Cryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:1) -

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Basic information

Entry
Database: PDB / ID: 9nnb
TitleCryo-EM structure of the Retron Ec78 complex, PtuA:PtuB:RT (4:2:1)
Components
  • (Retron I-A effector ...) x 2
  • DNA (73-MER)
  • RNA (41-MER)
  • Retron I-A Ec78 reverse transcriptase
KeywordsDNA-RNA HYBRID / Retron / msDNA / ncRNA
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / endonuclease activity / defense response to virus / ATP hydrolysis activity / RNA binding / ATP binding
Similarity search - Function
: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. ...: / : / Retron Ec78 putative HNH endonuclease-like / AAA domain, putative AbiEii toxin, Type IV TA system / RNA-directed DNA polymerase (reverse transcriptase), msDNA / : / ATPase, AAA-type, core / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / DNA / DNA (> 10) / RNA / RNA (> 10) / RNA-directed DNA polymerase / 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: 2.75 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: Structural 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: Retron I-A effector PtuA
D: Retron I-A effector PtuA
E: Retron I-A effector PtuA
F: Retron I-A effector PtuA
J: Retron I-A effector PtuB
N: DNA (73-MER)
B: Retron I-A Ec78 reverse transcriptase
L: RNA (41-MER)
K: Retron I-A effector PtuB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,12214
Polymers384,7109
Non-polymers1,4125
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

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Retron I-A effector ... , 2 types, 6 molecules CDEFJK

#1: Protein
Retron I-A effector PtuA


Mass: 62466.781 Da / Num. of mol.: 4
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: 26879.172 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

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DNA chain / Protein / RNA chain , 3 types, 3 molecules NBL

#3: DNA chain DNA (73-MER)


Mass: 24120.449 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)
#4: Protein Retron I-A Ec78 reverse transcriptase


Mass: 35538.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: NCTC8603_01325 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB38GW94
#5: RNA chain RNA (41-MER)


Mass: 21425.598 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) / References: GenBank: 437205

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Non-polymers , 2 types, 5 molecules

#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Details

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: Rectron Ec78 complex / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1250 mMsodium clorideNaCl1
225 mMTrisTris1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.2_5419 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140378 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007226107
ELECTRON MICROSCOPYf_angle_d0.84735765
ELECTRON MICROSCOPYf_chiral_restr0.05643986
ELECTRON MICROSCOPYf_plane_restr0.02254217
ELECTRON MICROSCOPYf_dihedral_angle_d17.3284576

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