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- EMDB-65147: Cryo-EM structure of retron Ec78 effector protein PtuA hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-65147
TitleCryo-EM structure of retron Ec78 effector protein PtuA hexamer
Map data
Sample
  • Complex: Cryo-EM structure of retron Ec78 effector protein PtuA hexamer
    • Protein or peptide: Retron Ec78 probable ATPase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsprokaryotic anti-phage immune elements / retron Ec78 / Septu / effector proteins / ATPase domain / TOXIN
Function / homology
Function and homology information


DNA synthesis involved in DNA repair / double-strand break repair / defense response to virus / ATP hydrolysis activity / ATP binding
Similarity search - Function
: / AAA domain, putative AbiEii toxin, Type IV TA system / ATPase, AAA-type, core / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Retron Ec78 probable ATPase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsDuan L / Chen L / Li S / Zhang K / Qing G
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural insights into the assembly and function of Retron Ec78 PtuAB
Authors: Duan L / Chen L
History
DepositionJun 24, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65147.png

Downloads & links

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Map

FileDownload / File: emd_65147.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.5616238 - 2.627939
Average (Standard dev.)0.000050702987 (±0.04562712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65147_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65147_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of retron Ec78 effector protein PtuA hexamer

EntireName: Cryo-EM structure of retron Ec78 effector protein PtuA hexamer
Components
  • Complex: Cryo-EM structure of retron Ec78 effector protein PtuA hexamer
    • Protein or peptide: Retron Ec78 probable ATPase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of retron Ec78 effector protein PtuA hexamer

SupramoleculeName: Cryo-EM structure of retron Ec78 effector protein PtuA hexamer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 370 KDa

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Macromolecule #1: Retron Ec78 probable ATPase

MacromoleculeName: Retron Ec78 probable ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 51.854594 KDa
Recombinant expressionOrganism: Expression vector pET-mod (others)
SequenceString: MTKQYERKAK GGNLLSAFEL YQRNTDNMPG LGEMLVDEWF ETCRDYIQDG HVDESGTFRP DNAFYLRRLT LKDFRRFSLL EIKFEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE LTDIKNDAEN RYADVSSTFF FGKGLKSVPI R LSRSALGT ...String:
MTKQYERKAK GGNLLSAFEL YQRNTDNMPG LGEMLVDEWF ETCRDYIQDG HVDESGTFRP DNAFYLRRLT LKDFRRFSLL EIKFEEDLT VIIGNNGKGK TSILYAIAKT LSWFVANILK EGGSGQRLSE LTDIKNDAEN RYADVSSTFF FGKGLKSVPI R LSRSALGT AERRDSEVKP ARDLADIWRV INEAKTINLP TFALYNVERS QPFNRNTKDN AGRREERFDA YSQALGGAGR FD HFVEWYI YLHKRTISDI SSSIKELEQQ VNDLQRSVDG GMVSVKSLLE QMKLKLSEAS ERNDAAVSSK MVTESVQKSI VEK SICSVV PSISKIWVEM TTGSDLVKVT NDGHDVTIDQ LSDGQRVFLS LVADLARRMV MLNPLLENPL EGRGIVLIDE IELH LHPKW QQEVILNLRS VFPNIQFIIT THSPIVLSTI EKRCIREFDP NDDGNQSFLD S

UniProtKB: Retron Ec78 probable ATPase

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 324895
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.3) / Number images used: 196999
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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