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- EMDB-40779: Structure of E. coli PtuA hexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-40779
TitleStructure of E. coli PtuA hexamer
Map data
Sample
  • Complex: PtuA
    • Protein or peptide: PtuA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsPtuA / anti-phage / Septu system / Immune System
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsShen ZF / Yang XY / Fu TM
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
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
DepositionMay 13, 2023-
Header (metadata) releaseJan 10, 2024-
Map releaseJan 10, 2024-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40779.png

Downloads & links

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Map

FileDownload / File: emd_40779.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 240 pix.
= 268.8 Å		1.12 Å/pix.
x 240 pix.
= 268.8 Å		1.12 Å/pix.
x 240 pix.
= 268.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-4.1881504 - 6.175743
Average (Standard dev.)-0.00025659084 (±0.11372499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_40779_additional_1.map
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Half map: #2

Fileemd_40779_half_map_1.map
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Half map: #1

Fileemd_40779_half_map_2.map
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Sample components

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Entire : PtuA

EntireName: PtuA
Components
  • Complex: PtuA
    • Protein or peptide: PtuA
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: PtuA

SupramoleculeName: PtuA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: 6 PtuA protomer form a hexamer.
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: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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 / 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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 779494
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
FSC plot (resolution estimation)

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