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- EMDB-28048: Structure of focused PtuA(dimer) and PtuB(monomer) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28048
TitleStructure of focused PtuA(dimer) and PtuB(monomer) complex
Map data
Sample
  • Complex: 6 ptuA form as a complex
    • Protein or peptide: PtuA
  • Protein or peptide: PtuB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPtuA / IMMUNE SYSTEM
Function / homologyRetron Ec78 putative HNH endonuclease-like / TIGR02646 family protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsShen ZF / Fu TM
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: PtuA and PtuB assemble into an inflammasome-like oligomer for anti-phage defense.
Authors: Yuanyuan Li / Zhangfei Shen / Mengyuan Zhang / Xiao-Yuan Yang / Sean P Cleary / Jiale Xie / Ila A Marathe / Marius Kostelic / Jacelyn Greenwald / Anthony D Rish / Vicki H Wysocki / Chong ...Authors: Yuanyuan Li / Zhangfei Shen / Mengyuan Zhang / Xiao-Yuan Yang / Sean P Cleary / Jiale Xie / Ila A Marathe / Marius Kostelic / Jacelyn Greenwald / Anthony D Rish / Vicki H Wysocki / Chong Chen / Qiang Chen / Tian-Min Fu / Yamei Yu /
Abstract: Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show ...Escherichia coli Septu system, an anti-phage defense system, comprises two components: PtuA and PtuB. PtuA contains an ATPase domain, while PtuB is predicted to function as a nuclease. Here we show that PtuA and PtuB form a stable complex with a 6:2 stoichiometry. Cryo-electron microscopy structure of PtuAB reveals a distinctive horseshoe-like configuration. PtuA adopts a hexameric arrangement, organized as an asymmetric trimer of dimers, contrasting the ring-like structure by other ATPases. Notably, the three pairs of PtuA dimers assume distinct conformations and fulfill unique roles in recruiting PtuB. Our functional assays have further illuminated the importance of the oligomeric assembly of PtuAB in anti-phage defense. Moreover, we have uncovered that ATP molecules can directly bind to PtuA and inhibit the activities of PtuAB. Together, the assembly and function of the Septu system shed light on understanding other ATPase-containing systems in bacterial immunity.
History
DepositionSep 6, 2022-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28048.png

Downloads & links

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Map

FileDownload / File: emd_28048.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.454
Minimum - Maximum-2.4635856 - 4.1224747
Average (Standard dev.)-0.00053283013 (±0.085238956)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 286.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_28048_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28048_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28048_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 6 ptuA form as a complex

EntireName: 6 ptuA form as a complex
Components
  • Complex: 6 ptuA form as a complex
    • Protein or peptide: PtuA
  • Protein or peptide: PtuB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: 6 ptuA form as a complex

SupramoleculeName: 6 ptuA form as a complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: PtuA

MacromoleculeName: PtuA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 53.189656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRIDKLSLLN FRCFKQLDIT FDEHITILVA PNGAGKTTVL DAVRLALFPF IRGFDASLYV KDKSLAIRTE DLRLIYRQEA LNMEMSSPA KITATGEWAS GKTATWMLDK RGEQPPHEDK MAAQLTRWGE QLQKRVREEH SLQQVELPLM LYLGTARLWY Q ERYEKQPT ...String:
MRIDKLSLLN FRCFKQLDIT FDEHITILVA PNGAGKTTVL DAVRLALFPF IRGFDASLYV KDKSLAIRTE DLRLIYRQEA LNMEMSSPA KITATGEWAS GKTATWMLDK RGEQPPHEDK MAAQLTRWGE QLQKRVREEH SLQQVELPLM LYLGTARLWY Q ERYEKQPT EQRLDNSAFS RLSGYDDCLS ATSNYKQFEQ WYSWLWLSYR EHQITQLESP SAKLKEGVRV QRMKEAIQAI QQ AINCLTQ QVTGWHDLEY SASHNQQLVM SHPQYGKIPL SQLSDGLRNA VAMVADIAFR CVKLNPHLQN DAALKTQGIV LID EVDMFL HPAWQQQIIQ SLRSAFPQIQ FIVTTHSPQV LSTVKRESIR LLEQDENGNG KALMPLGATY GEPSNDVLQS VMGV DPQPA VKEKADLQKL TGWVDQGKYD EPKTQQLMVA LEVALGEKHP QLQRLQRSIA RQRLLKGKAQ

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Macromolecule #2: PtuB

MacromoleculeName: PtuB / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.136291 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRHVIKTQLG TVALLTAHEN PPQDADQSTR RWRNFRRDKA AVMVQLINEQ YHLCCYSEIR SDLRGLGYHI EHVENKSQHP ERTFDYQNL AASALDSGEN GGLSSLKGKN AFGGHAQGKQ DVVDMAKFIH CHIRDCSRYF AYLSDGRIVP ADELNAQETE N AQYTIDLL ...String:
MRHVIKTQLG TVALLTAHEN PPQDADQSTR RWRNFRRDKA AVMVQLINEQ YHLCCYSEIR SDLRGLGYHI EHVENKSQHP ERTFDYQNL AASALDSGEN GGLSSLKGKN AFGGHAQGKQ DVVDMAKFIH CHIRDCSRYF AYLSDGRIVP ADELNAQETE N AQYTIDLL NLNSGFLQTE RRNHWEELEQ LFDEHIEKDW DLQQLLQLDL VSTPDHKLHE FFSITRQFFQ QEAEQVLQSH AP ALI

UniProtKB: TIGR02646 family protein

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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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

Concentration1.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1832915
FSC plot (resolution estimation)

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