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- EMDB-53443: E. coli JetABC dimer in a DNA boarding state -

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Basic information

Entry
Database: EMDB / ID: EMD-53443
TitleE. coli JetABC dimer in a DNA boarding state
Map dataSharp map
Sample
  • Complex: JetABC DNA boarding state, a step of the loading reaction on DNA
    • Protein or peptide: JetB
    • Protein or peptide: JetA
    • Protein or peptide: JetC
    • DNA: Biotinylated circular plasmid DNA (1894-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION
KeywordsSMC complexes / Wadjet / JetABCD / DNA loop extrusion / DNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRoisne-Hamelin F / Gruber S
Funding supportEuropean Union, Switzerland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)724482European Union
Swiss National Science Foundation10001017 Switzerland
CitationJournal: Molecular Cell / Year: 2025
Title: Mechanism of DNA Entrapment by a Loop-Extruding Wadjet SMC Motor
Authors: Roisne-Hamelin F / Liu HW / Gruber S
History
DepositionApr 16, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53443.png

Downloads & links

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Map

FileDownload / File: emd_53443.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 400 pix.
= 466.56 Å		1.17 Å/pix.
x 400 pix.
= 466.56 Å		1.17 Å/pix.
x 400 pix.
= 466.56 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.31
Minimum - Maximum-1.9707875 - 2.9768455
Average (Standard dev.)0.00050614245 (±0.061175525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 466.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53443_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Full EM map

Fileemd_53443_additional_1.map
AnnotationFull EM map
Projections & Slices
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Half map: Half map A

Fileemd_53443_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_53443_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Sample components

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Entire : JetABC DNA boarding state, a step of the loading reaction on DNA

EntireName: JetABC DNA boarding state, a step of the loading reaction on DNA
Components
  • Complex: JetABC DNA boarding state, a step of the loading reaction on DNA
    • Protein or peptide: JetB
    • Protein or peptide: JetA
    • Protein or peptide: JetC
    • DNA: Biotinylated circular plasmid DNA (1894-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: JetABC DNA boarding state, a step of the loading reaction on DNA

SupramoleculeName: JetABC DNA boarding state, a step of the loading reaction on DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: E. coli JetABC was incubated with biotinylated plasmid DNA in presence of ATP. The reaction was poisoned with beryllium fluoride prior grid freezing.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3

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Macromolecule #1: JetB

MacromoleculeName: JetB / type: protein_or_peptide / ID: 1
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3
Molecular weightTheoretical: 28.020416 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAGFFDKLIN RSVTANAGCE PEPSDEEVTD ESVEDSLASS ETRTLQKIRE ATQELLKYGL LEEASKPNLY RIVLSHPEEV TRILEPLDL DIGIDEIRGL LYVKVRLDET PAQDEWAHPL VRRQRLNLEQ SLLVAILRQH FVAWEQESGT GASQAQIAID D LLPQLQIY ...String:
MAGFFDKLIN RSVTANAGCE PEPSDEEVTD ESVEDSLASS ETRTLQKIRE ATQELLKYGL LEEASKPNLY RIVLSHPEEV TRILEPLDL DIGIDEIRGL LYVKVRLDET PAQDEWAHPL VRRQRLNLEQ SLLVAILRQH FVAWEQESGT GASQAQIAID D LLPQLQIY LGDPGSESKE RTRLLTLLDQ LKGHGLVTSP DAHERIVIRP IIAHLADPIN LQALLAWLRE QIAQQTSPND AP EKDSSEE DVG

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Macromolecule #2: JetA

MacromoleculeName: JetA / type: protein_or_peptide / ID: 2
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar. "GPAA" at the begining of the theorical sequence is the remaining of the purification tag after tag cleavage. The ...Details: The last "G" in the theorical sequence is the result of a DNA cloning scar. "GPAA" at the begining of the theorical sequence is the remaining of the purification tag after tag cleavage. The last "G" in the theorical sequence is the result of a DNA cloning scar.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3
Molecular weightTheoretical: 57.81891 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GPAAMEENTR QRTENYISAK NQHPAWILLA TRRAPLVLSC LKTLFEKSHD GIPLEEAIQS LSSILIEHVS QEQYDINQDN PFLQASREL REWIKRRLIV ERDGRIFATD ALEVAITFVE SLDNRFMTST ASRLSTVQRE IENLETRLNP NPANRVATLR R RISELERE ...String:
GPAAMEENTR QRTENYISAK NQHPAWILLA TRRAPLVLSC LKTLFEKSHD GIPLEEAIQS LSSILIEHVS QEQYDINQDN PFLQASREL REWIKRRLIV ERDGRIFATD ALEVAITFVE SLDNRFMTST ASRLSTVQRE IENLETRLNP NPANRVATLR R RISELERE LQEAEAGHIE VLETHQAVEH IRDVYNLASS LRADFRRVED SWREADRALR QSIIGEQYHR GDIVERLLND QD ALLNTPE GRVFDSFQQQ LRQSSELKAM SERLRVILSH PSASDALNRL QRHDLRWLVK RLVDESQTVL QARARSERDV RGF MKTGLA AEHHRVGHLL NEFLNLALKL DWQRQMIRKQ EVPLPAVGVA VTGIPAIERL RFKEVDDEAE QTLDLSNHAA DLTQ IGDDF WDAFNGLDRE VLIQQTLQLL AKENRPVGLA ELAELLPPAH DLETFAVWIG MAREAGIEVI DSQREFAELS DGEGR RWRF NLPTTGLESQ ALMDIDWEG

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Macromolecule #3: JetC

MacromoleculeName: JetC / type: protein_or_peptide / ID: 3
Details: The last "G" in the theorical sequence is the result of a DNA cloning scar.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3
Molecular weightTheoretical: 124.562938 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MNQVSGLAGK ESFILTRIEL FNWGGFHGLH QAAIHQDGTA VIGPTGSGKT TLVDALMTLL CANPRYNLAS TGGHESDRDL ISYVRGVSG PGDGGEGQSH IARPGKTVTG IAATLEREGK QVRLGALLWF DSTSSSVTDM KRLWLFSDNP GQTLEHWLNV Y HEGGTRLL ...String:
MNQVSGLAGK ESFILTRIEL FNWGGFHGLH QAAIHQDGTA VIGPTGSGKT TLVDALMTLL CANPRYNLAS TGGHESDRDL ISYVRGVSG PGDGGEGQSH IARPGKTVTG IAATLEREGK QVRLGALLWF DSTSSSVTDM KRLWLFSDNP GQTLEHWLNV Y HEGGTRLL RQMEKEAIGL WTYPNKKQYL ARLRDFFEVG ENAFTLLNRA AGLKQLNSID EIFRELVLDD HSAFDRAAEV AN SFDGLTE IHQELETARK QQQSLQPVAL SWEKYQKQER QLADWLTLES LLPLWFAQQA SHLWREKINL LNARLAEAQT SEE QLQSQL DLQKKVVSDC MQRYLQVGGA NIDELNERIK DWQKTLGSRE ALARQYQQLT RNLGLPSDLS QPQLEANQHE AEAR CEQIA VDIKLKQEEA YQKGALSHHI TEELRERENE RAEIARRPDS NLPAHYQAFR SELAKALNVD ESELPFVAEL IQVKP EEAQ WRGAIERAVG SNRLRILVAP ESAQEALRWV NQRNNRLHVR LLEVKLPHSP ARFFDDGFTR KLLWKDHPWR EAVKAL LAE SDRHCVDSPE QLHDTPHAMT VQGLMSGKQR FYDKHDQKRL DEDWLTGFDN RDRLNFLAKE IATLQEQVKT ANAAFEF AK GEVGLLQNQA ASFQKIEQID FDSIDVPGAK SQLDALRERL ENLTRPDSDA SVAKAKLDEA QTIESELDKQ LRAANKVT N VLDTELTLAR AAERKAQQTA QQGMKEEERE LCASHFPVVT LEQLPDIRDL ERQHERGIQH EIERVKAELH RLNIELTKR MSEAKRVDTG ALVEAGADLD DIPVYLQRLQ ELTEEALPEK LNRFLDYLNR SSDDGVTQLL SHIEHEVLVI EERLNELNET MFRVDFQPD RYLRLDTKKV VHESLRTLEK AQRQLNAARF VDDNGESHYK ALQVLVAQLR DACERNRTLG AKALLDPRFR L EFAVSVMD RQSGNVIESR TGSQGGSGGE KEIIASYVLT ASLSYALCPA GSRYPLFGTI ILDEAFSRSS HAVAGRIIAA LR EFGLHAV FITPNKEMRL LRDHTRSAIV VHRRGQNSNM ASLSWEELER HYQRRGNAG

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Macromolecule #4: Biotinylated circular plasmid DNA (1894-MER)

MacromoleculeName: Biotinylated circular plasmid DNA (1894-MER) / type: dna / ID: 4
Details: Only a portion of the biotinylated plasmid (pSG7427, 1894bp) has been modelled as polyAT track, because the complex is expected to load at random positions and the local resolution of the ...Details: Only a portion of the biotinylated plasmid (pSG7427, 1894bp) has been modelled as polyAT track, because the complex is expected to load at random positions and the local resolution of the DNA does not allow any sequence assignment.
Number of copies: 2 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.477025 KDa
SequenceString: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (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 #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 31601 / Average electron dose: 39.48 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.6) / Number images used: 57494
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8as8

source_name: PDB, initial_model_type: experimental model

8bfn

source_name: PDB, initial_model_type: experimental model

8q72

source_name: PDB, initial_model_type: experimental model
source_name: Other, initial_model_type: in silico modelIdealized B-form DNA was flexibly fitted
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9qxs:
E. coli JetABC dimer in a DNA boarding state

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