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- EMDB-10400: Stalled FtsK motor domain bound to dsDNA -

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Basic information

Entry
Database: EMDB / ID: EMD-10400
TitleStalled FtsK motor domain bound to dsDNA
Map data
Sample
  • Complex: FtsK motor domain with dsDNA, stalled state
    • Complex: FtsK motor domain
      • Protein or peptide: DNA translocase FtsK
    • Complex: DNA
      • DNA: dsDNA substrate
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsDNA translocation / DNA motor / RecA fold / Divisome / DNA BINDING PROTEIN
Function / homology
Function and homology information


DNA translocase activity / cellular response to antibiotic / chromosome segregation / cell division / DNA binding / ATP binding / plasma membrane
Similarity search - Function
FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / : / FtsK domain / FtsK/SpoIIIE family ...FtsK gamma domain / DNA translocase FtsK, 4TM region / FtsK alpha domain / Ftsk gamma domain / 4TM region of DNA translocase FtsK/SpoIIIE / FtsK alpha domain / Ftsk_gamma / : / FtsK domain / FtsK/SpoIIIE family / FtsK domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA translocase FtsK
Similarity search - Component
Biological speciesPseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) / synthetic construct (others) / Pseudomonas aeruginosa PAO1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.34 Å
AuthorsJean NL / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
European Molecular Biology OrganizationALTF-128-2016
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2020
Title: FtsK in motion reveals its mechanism for double-stranded DNA translocation.
Authors: Nicolas L Jean / Trevor J Rutherford / Jan Löwe /
Abstract: FtsK protein contains a fast DNA motor that is involved in bacterial chromosome dimer resolution. During cell division, FtsK translocates double-stranded DNA until both recombination sites are ...FtsK protein contains a fast DNA motor that is involved in bacterial chromosome dimer resolution. During cell division, FtsK translocates double-stranded DNA until both recombination sites are placed at mid cell for subsequent dimer resolution. Here, we solved the 3.6-Å resolution electron cryo-microscopy structure of the motor domain of FtsK while translocating on its DNA substrate. Each subunit of the homo-hexameric ring adopts a unique conformation and one of three nucleotide states. Two DNA-binding loops within four subunits form a pair of spiral staircases within the ring, interacting with the two DNA strands. This suggests that simultaneous conformational changes in all ATPase domains at each catalytic step generate movement through a mechanism related to filament treadmilling. While the ring is only rotating around the DNA slowly, it is instead the conformational states that rotate around the ring as the DNA substrate is pushed through.
#1: Journal: Biorxiv
Title: FtsK in motion reveals its mechanism for double-stranded DNA translocation
Authors: Jean NL / Rutherford TJ / Lowe J
History
DepositionOct 24, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t8g
  • Surface level: 0.0205
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10400.png

Downloads & links

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Map

FileDownload / File: emd_10400.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 240 pix.
= 251.52 Å		1.05 Å/pix.
x 240 pix.
= 251.52 Å		1.05 Å/pix.
x 240 pix.
= 251.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0205 / Movie #1: 0.0205
Minimum - Maximum-0.044834834 - 0.07722655
Average (Standard dev.)0.00032100076 (±0.0030821827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 251.51999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0481.0481.048
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z251.520251.520251.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0450.0770.000

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Supplemental data

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Sample components

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Entire : FtsK motor domain with dsDNA, stalled state

EntireName: FtsK motor domain with dsDNA, stalled state
Components
  • Complex: FtsK motor domain with dsDNA, stalled state
    • Complex: FtsK motor domain
      • Protein or peptide: DNA translocase FtsK
    • Complex: DNA
      • DNA: dsDNA substrate
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: FtsK motor domain with dsDNA, stalled state

SupramoleculeName: FtsK motor domain with dsDNA, stalled state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: FtsK motor domain

SupramoleculeName: FtsK motor domain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DNA translocase FtsK

MacromoleculeName: DNA translocase FtsK / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 54.001441 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVPDRREQSK AKERLLEREE ALAKHMSERE KRPPPKIDPP PSPKAPEPSK RVLKEKQAPL FVDTAVEGTL PPLSLLDPAE VKQKSYSPE SLEAMSRLLE IKLKEFGVEV SVDSVHPGPV ITRFEIQPAA GVKVSRISNL AKDLARSLAV ISVRVVEVIP G KTTVGIEI ...String:
MVPDRREQSK AKERLLEREE ALAKHMSERE KRPPPKIDPP PSPKAPEPSK RVLKEKQAPL FVDTAVEGTL PPLSLLDPAE VKQKSYSPE SLEAMSRLLE IKLKEFGVEV SVDSVHPGPV ITRFEIQPAA GVKVSRISNL AKDLARSLAV ISVRVVEVIP G KTTVGIEI PNEDRQMVRF SEVLSSPEYD EHKSTVPLAL GHDIGGRPII TDLAKMPHLL VAGTTGSGKS VGVNAMLLSI LF KSTPSEA RLIMIDPKML ELSIYEGIPH LLCPVVTDMK EAANALRWSV AEMERRYRLM AAMGVRNLAG FNRKVKDAEE AGT PLTDPL FRRESPDDEP PQLSTLPTIV VVVDEFADMM MIVGKKVEEL IARIAQKARA AGIHLILATQ RPSVDVITGL IKAN IPTRI AFQVSSKIDS RTILDQGGAE QLLGHGDMLY LPPGTGLPIR VHGAFVSDDE VHRVVEAWKL RGAPDYIEDI LAGVD EGGK LHHHHHH

UniProtKB: DNA translocase FtsK

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Macromolecule #2: dsDNA substrate

MacromoleculeName: dsDNA substrate / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.894239 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationName
25.0 mMTris
2.0 mMATPgammaS
4.0 mMMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details0.7 m/mL FtsK 1.5 uM 45 bp DNA

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 3300 / Average electron dose: 42.95 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2iuu


Details: 40 A low-pass filtered map generated from PDB 2IUU
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 47319
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2iuu


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6t8g:
Stalled FtsK motor domain bound to dsDNA

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