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- EMDB-10399: FtsK motor domain with dsDNA, translocating state -

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Basic information

Entry
Database: EMDB / ID: EMD-10399
TitleFtsK motor domain with dsDNA, translocating state
Map data
Sample
  • Complex: FtsK motor domain with dsDNA, translocating state
    • Complex: FtsK motor domain
      • Protein or peptide: DNA translocase FtsK
    • Complex: DNA
      • DNA: dsDNA substrate
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


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 domain profile. ...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: 3.65 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-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6t8b
  • Surface level: 0.0305
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10399.png

Downloads & links

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Map

FileDownload / File: emd_10399.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.048 Å
Density
Contour LevelBy AUTHOR: 0.0305 / Movie #1: 0.0305
Minimum - Maximum-0.08707282 - 0.13402638
Average (Standard dev.)0.0003072867 (±0.00420755)
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-0.0870.1340.000

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Supplemental data

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Sample components

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Entire : FtsK motor domain with dsDNA, translocating state

EntireName: FtsK motor domain with dsDNA, translocating state
Components
  • Complex: FtsK motor domain with dsDNA, translocating state
    • Complex: FtsK motor domain
      • Protein or peptide: DNA translocase FtsK
    • Complex: DNA
      • DNA: dsDNA substrate
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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

SupramoleculeName: FtsK motor domain with dsDNA, translocating 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)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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)
Recombinant expressionOrganism: 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

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Macromolecule #2: dsDNA substrate

MacromoleculeName: dsDNA substrate / type: dna / ID: 2
Details: Sequence not determined due to sequence heterogeneity of the protein-bound DNA
Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.129039 KDa
SequenceString:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 3 / 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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Macromolecule #4: MAGNESIUM ION

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

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

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

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

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2iuu


Details: 40 A low-pass filtered map generated from PDB 2IUU
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 56485
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2iuu


Chain - Chain ID: A
Output model

PDB-6t8b:
FtsK motor domain with dsDNA, translocating state

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