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- EMDB-27797: Cryo-EM structure of bundle-forming pilus extension ATPase from E... -

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Entry
Database: EMDB / ID: EMD-27797
TitleCryo-EM structure of bundle-forming pilus extension ATPase from E.coli in the presence of ADP
Map data
Sample
  • Organelle or cellular component: Bundle-forming pilus extension ATPase from enteropathogenic E. coli in the presence of ADP
    • Protein or peptide: BfpD
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION
KeywordsBfpD / AAA-ATPase / Structural protein / Type 4 pilus accessory protein
Function / homologyType II/IV secretion system protein / Type II/IV secretion system protein / nucleotide binding / P-loop containing nucleoside triphosphate hydrolase / BfpD
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsNayak AR / Zhao J / Donnenberg MS / Samso M
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR068431 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116790 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R56A/111767 United States
CitationJournal: mBio / Year: 2022
Title: Cryo-EM Structure of the Type IV Pilus Extension ATPase from Enteropathogenic Escherichia coli.
Authors: Ashok R Nayak / Pradip K Singh / Jinlei Zhao / Montserrat Samsó / Michael S Donnenberg /
Abstract: Type 4 pili (T4P) are retractable surface appendages found on numerous bacteria and archaea that play essential roles in various microbial functions, including host colonization by pathogens. An ...Type 4 pili (T4P) are retractable surface appendages found on numerous bacteria and archaea that play essential roles in various microbial functions, including host colonization by pathogens. An ATPase is required for T4P extension, but the mechanism by which chemical energy is transduced to mechanical energy for pilus extension has not been elucidated. Here, we report the cryo-electron microscopy (cryo-EM) structure of the BfpD ATPase from enteropathogenic Escherichia coli (EPEC) in the presence of either ADP or a mixture of ADP and AMP-PNP. Both structures, solved at 3 Å resolution, reveal the typical toroid shape of AAA+ ATPases and unambiguous 6-fold symmetry. This 6-fold symmetry contrasts with the 2-fold symmetry previously reported for other T4P extension ATPase structures, all of which were from thermophiles and solved by crystallography. In the presence of the nucleotide mixture, BfpD bound exclusively AMP-PNP, and this binding resulted in a modest outward expansion in comparison to the structure in the presence of ADP, suggesting a concerted model for hydrolysis. molecular models reveal a partially open configuration of all subunits where the nucleotide binding site may not be optimally positioned for catalysis. ATPase functional studies reveal modest activity similar to that of other extension ATPases, while calculations indicate that this activity is insufficient to power pilus extension. Our results reveal that, despite similarities in primary sequence and tertiary structure, T4P extension ATPases exhibit divergent quaternary configurations. Our data raise new possibilities regarding the mechanism by which T4P extension ATPases power pilus formation. Type 4 pili are hairlike surface appendages on many bacteria and archaea that can be extended and retracted with tremendous force. They play a critical role in disease caused by several deadly human pathogens. Pilus extension is made possible by an enzyme that converts chemical energy to mechanical energy. Here, we describe the three-dimensional structure of such an enzyme from a human pathogen in unprecedented detail, which reveals a mechanism of action that has not been seen previously among enzymes that power type 4 pilus extension.
History
DepositionAug 7, 2022-
Header (metadata) releaseOct 26, 2022-
Map releaseOct 26, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27797.png

Downloads & links

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Map

FileDownload / File: emd_27797.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.375
Minimum - Maximum-1.5320714 - 2.5052748
Average (Standard dev.)0.0024771278 (±0.07665491)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27797_half_map_1.map
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Half map: #1

Fileemd_27797_half_map_2.map
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Sample components

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Entire : Bundle-forming pilus extension ATPase from enteropathogenic E. co...

EntireName: Bundle-forming pilus extension ATPase from enteropathogenic E. coli in the presence of ADP
Components
  • Organelle or cellular component: Bundle-forming pilus extension ATPase from enteropathogenic E. coli in the presence of ADP
    • Protein or peptide: BfpD
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Bundle-forming pilus extension ATPase from enteropathogenic E. co...

SupramoleculeName: Bundle-forming pilus extension ATPase from enteropathogenic E. coli in the presence of ADP
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: BfpD ATPase with 5 mM MgCl2 and 1 mM ADP
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 362 KDa

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Macromolecule #1: BfpD

MacromoleculeName: BfpD / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 60.440062 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVNKTEKTSD LMFERFKRNV SEIVTGDGGE LELTVEQRKY FLIFKNGDFL VSSCHMKHHL VQMLREIATR KGYPNLTIYE VNLKDIRLL YEASLKTVQN NGQDLLPVEK RASMLLFECA EMRVSDLHIK VYDAEADIYI RKDGDMELLR QIESNTAHSI L ASLYNNAD ...String:
MVNKTEKTSD LMFERFKRNV SEIVTGDGGE LELTVEQRKY FLIFKNGDFL VSSCHMKHHL VQMLREIATR KGYPNLTIYE VNLKDIRLL YEASLKTVQN NGQDLLPVEK RASMLLFECA EMRVSDLHIK VYDAEADIYI RKDGDMELLR QIESNTAHSI L ASLYNNAD DSDATYKINA YQAARIVASK SRLALPPVIQ AVRLQFNPLG QGGRYLIARF LYTDKSEKQK EMDPTRFGFH HS HAESFSR MRNLPIGINI ISGPTGSGKS TTLKNLLELL YIEKKKKVNI ISIEDPPEYE IDGTAQLPIT NVETEAQRGE EYR KAITAA LRSDPDIIMP GEARDAEVIN LLFTAAMTGH QVWTSLHANN ALAIFDRLKD QGVDEFKLTD PELITGLVAQ RLVR KLCAQ CSITLTEYIA SGGGISDTDR KIISGHETSV RFPNPRAKKC CRDGYNGRTI LAEVIEPDSK LLRLVAEGKR EDAQH YWLT SLHGMALKEH AWLKIISGEI CVMDAVNKIS GIDNITEERK KYLFSRDNEI

UniProtKB: BfpD

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration4.0 mg/mL
BufferpH: 7.6
Details: 20 mM Tris (pH 7.6), 0.1 mM NaCl, 1 mM ADP, 5 mM MgCl2, 2 mM DTT, 0.5 mM CHAPSO
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 8387 / Average electron dose: 60.0 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: 1.0 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1135477
Startup modelType of model: NONE / Details: Ab-initio reconstruction in cryosparc 2.15
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 317950
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8dzg:
Cryo-EM structure of bundle-forming pilus extension ATPase from E.coli in the presence of ADP

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