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- EMDB-28049: Structure of E.coli Septu (PtuAB) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-28049
TitleStructure of E.coli Septu (PtuAB) complex
Map data
Sample
  • Complex: 6 PtuA and 2 PtuB form as a complex
    • Protein or peptide: PtuA
    • Protein or peptide: PtuB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPtuA / PtuB Septu / 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: 2.6 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) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28049.png

Downloads & links

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Map

FileDownload / File: emd_28049.map.gz / Format: CCP4 / Size: 127.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 326 pix.
= 365.12 Å		1.12 Å/pix.
x 301 pix.
= 337.12 Å		1.12 Å/pix.
x 341 pix.
= 381.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-3.5442681 - 8.034378
Average (Standard dev.)0.0010495207 (±0.07244442)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-22-42-36
Dimensions301341326
Spacing341301326
CellA: 381.92 Å / B: 337.12 Å / C: 365.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_28049_additional_1.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 : 6 PtuA and 2 PtuB form as a complex

EntireName: 6 PtuA and 2 PtuB form as a complex
Components
  • Complex: 6 PtuA and 2 PtuB form as a complex
    • Protein or peptide: PtuA
    • Protein or peptide: PtuB
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: 6 PtuA and 2 PtuB form as a complex

SupramoleculeName: 6 PtuA and 2 PtuB form as a complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 6 / 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: 2 / 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: 4 / 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

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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2307662
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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