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- EMDB-12515: Vibrio cholerae ParA2-ATPyS-DNA filament -

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Basic information

Entry
Database: EMDB / ID: EMD-12515
TitleVibrio cholerae ParA2-ATPyS-DNA filament
Map data
Sample
  • Complex: ParA2-ATPgS-DNA
    • Protein or peptide: AAA family ATPase
    • DNA: DNA (49-MER)
    • DNA: DNA (49-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
Function / homologyParA helix turn helix domain / ParA helix turn helix domain / : / AAA domain / AAA domain / P-loop containing nucleoside triphosphate hydrolase / AAA family ATPase
Function and homology information
Biological speciesVibrio cholerae (bacteria) / Neoarius leptaspis (salmon catfish)
Methodhelical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsParker AV / Bergeron JRC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Not funded United Kingdom
CitationJournal: Nat Commun / Year: 2021
Title: The structure of the bacterial DNA segregation ATPase filament reveals the conformational plasticity of ParA upon DNA binding.
Authors: Alexandra V Parker / Daniel Mann / Svetomir B Tzokov / Ling C Hwang / Julien R C Bergeron /
Abstract: The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of ...The efficient segregation of replicated genetic material is an essential step for cell division. Bacterial cells use several evolutionarily-distinct genome segregation systems, the most common of which is the type I Par system. It consists of an adapter protein, ParB, that binds to the DNA cargo via interaction with the parS DNA sequence; and an ATPase, ParA, that binds nonspecific DNA and mediates cargo transport. However, the molecular details of how this system functions are not well understood. Here, we report the cryo-EM structure of the Vibrio cholerae ParA2 filament bound to DNA, as well as the crystal structures of this protein in various nucleotide states. These structures show that ParA forms a left-handed filament on DNA, stabilized by nucleotide binding, and that ParA undergoes profound structural rearrangements upon DNA binding and filament assembly. Collectively, our data suggest the structural basis for ParA's cooperative binding to DNA and the formation of high ParA density regions on the nucleoid.
History
DepositionFeb 26, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateOct 20, 2021-
Current statusOct 20, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7npf
  • Surface level: 1.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7npf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12515.png

Downloads & links

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Map

FileDownload / File: emd_12515.map.gz / Format: CCP4 / Size: 14.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.04 Å/pix.
x 140 pix.
= 145.6 Å		1.04 Å/pix.
x 137 pix.
= 142.48 Å		1.04 Å/pix.
x 200 pix.
= 208. 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: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.4 / Movie #1: 1.4
Minimum - Maximum-7.984454 - 11.601824
Average (Standard dev.)5.259768e-12 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin29029
Dimensions137200140
Spacing140137200
CellA: 145.59999 Å / B: 142.48 Å / C: 208.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z140137200
origin x/y/z0.0000.0000.000
length x/y/z145.600142.480208.000
α/β/γ90.00090.00090.000
start NX/NY/NZ29290
NX/NY/NZ140137200
MAP C/R/S321
start NC/NR/NS02929
NC/NR/NS200137140
D min/max/mean-7.98411.6020.000

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Supplemental data

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Sample components

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Entire : ParA2-ATPgS-DNA

EntireName: ParA2-ATPgS-DNA
Components
  • Complex: ParA2-ATPgS-DNA
    • Protein or peptide: AAA family ATPase
    • DNA: DNA (49-MER)
    • DNA: DNA (49-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: ParA2-ATPgS-DNA

SupramoleculeName: ParA2-ATPgS-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Macromolecule #1: AAA family ATPase

MacromoleculeName: AAA family ATPase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 46.440969 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAMKREQTIE NLYQLAQLTQ QVQADRIEIV LEERRDEHFP PMSKALMETR SGLTRRKLDE AIAKMEEAGH QFTKNNANHY SISLSEAHM LMDAAGVPKF HERKKNNENK PWIINVQNQK GGTGKSMTAV HLAACLALNL DKRYRICLID LDPQGSLRLF L NPQISLAE ...String:
MAMKREQTIE NLYQLAQLTQ QVQADRIEIV LEERRDEHFP PMSKALMETR SGLTRRKLDE AIAKMEEAGH QFTKNNANHY SISLSEAHM LMDAAGVPKF HERKKNNENK PWIINVQNQK GGTGKSMTAV HLAACLALNL DKRYRICLID LDPQGSLRLF L NPQISLAE HTNIYSAVDI MLDNVPDGVQ VDTEFLRKNV MLPTQYPNLK TISAFPEDAM FNAEAWQYLS QNQSLDIVRL LK EKLIDKI ASDFDIIMID TGPHVDPLVW NAMYASNALL IPCAAKRLDW ASTVNFFQHL PTVYEMFPED WKGLEFVRLM PTM FEDDNK KQVSVLTEMN YLLGDQVMMA TIPRSRAFET CADTYSTVFD LTVNDFEGGK KTLATAQDAV QKSALELERV LHSH WSSLN QG

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Macromolecule #2: DNA (49-MER)

MacromoleculeName: DNA (49-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Neoarius leptaspis (salmon catfish)
Molecular weightTheoretical: 15.30217 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)

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Macromolecule #3: DNA (49-MER)

MacromoleculeName: DNA (49-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Neoarius leptaspis (salmon catfish)
Molecular weightTheoretical: 14.86049 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 5 / Number of copies: 8 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.02 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 28.68 Å
Applied symmetry - Helical parameters - Δ&Phi: -80.57 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 182997
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7npe

Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-7npf:
Vibrio cholerae ParA2-ATPyS-DNA filament

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