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- EMDB-53445: JetABC DNA loaded state monomer (open) -

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Basic information

Entry
Database: EMDB / ID: EMD-53445
TitleJetABC DNA loaded state monomer (open)
Map dataSharp map
Sample
  • Complex: Middle-crosslinked JetABC loading on plasmid DNA
    • Protein or peptide: JetB
    • Protein or peptide: JetA
    • DNA: Circular plasmid DNA (1843-MER)
    • Protein or peptide: JetC
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsSMC complexes / Wadjet / JetABCD / DNA loop extrusion / DNA BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.57 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_53445.png

Downloads & links

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Map

FileDownload / File: emd_53445.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.)
1.16 Å/pix.
x 400 pix.
= 464.64 Å		1.16 Å/pix.
x 400 pix.
= 464.64 Å		1.16 Å/pix.
x 400 pix.
= 464.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1616 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.147
Minimum - Maximum-0.37831745 - 0.78306
Average (Standard dev.)0.000010551454 (±0.018771278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 464.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53445_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full EM map

Fileemd_53445_additional_1.map
AnnotationFull EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_53445_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_53445_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Middle-crosslinked JetABC loading on plasmid DNA

EntireName: Middle-crosslinked JetABC loading on plasmid DNA
Components
  • Complex: Middle-crosslinked JetABC loading on plasmid DNA
    • Protein or peptide: JetB
    • Protein or peptide: JetA
    • DNA: Circular plasmid DNA (1843-MER)
    • Protein or peptide: JetC
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Middle-crosslinked JetABC loading on plasmid DNA

SupramoleculeName: Middle-crosslinked JetABC loading on plasmid DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: E. coli cysteine-less JetABC crosslinked at the "middle" position was incubated with plasmid DNA in presence of ATP 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3
Molecular weightTheoretical: 28.00435 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MAGFFDKLIN RSVTANAGSE PEPSDEEVTD ESVEDSLASS ETRTLQKIRE ATQELLKYGL LEEASKPNLY RIVLSHPEEV TRILEPLDL DIGIDEIRGL LYVKVRLDET PAQDEWAHPL VRRQRLNLEQ SLLVAILRQH FVAWEQESGT GASQAQIAID D LLPQLQIY ...String:
MAGFFDKLIN RSVTANAGSE 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: 57.786848 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GPAAMEENTR QRTENYISAK NQHPAWILLA TRRAPLVLSA LKTLFEKSHD GIPLEEAIQS LSSILIEHVS QEQYDINQDN PFLQASREL REWIKRRLIV ERDGRIFATD ALEVAITFVE SLDNRFMTST ASRLSTVQRE IENLETRLNP NPANRVATLR R RISELERE ...String:
GPAAMEENTR QRTENYISAK NQHPAWILLA TRRAPLVLSA 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 #4: JetC

MacromoleculeName: JetC / type: protein_or_peptide / ID: 4
Details: 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: 124.570797 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MNQVSGLAGK ESFILTRIEL FNWGGFHGLH QAAIHQDGTA VIGPTGSGKT TLVDALMTLL LANPRYNLAS TGGHESDRDL ISYVRGVSG PGDGGEGQSH IARPGKTVTG IAATLEREGK QVRLGALLWF DSTSSSVTDM KRLWLFSDNP GQTLEHWLNV Y HEGGTRLL ...String:
MNQVSGLAGK ESFILTRIEL FNWGGFHGLH QAAIHQDGTA VIGPTGSGKT TLVDALMTLL LANPRYNLAS 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 DLQKKVVSDH MQRYLQVGGA NIDELNERIK DWQKTLGSRE ALARQYQQLT RNLGLPSDLS QPQLEANQHE AEAR REQIA VDIKLKQEEA YQKGALSHHI TEELRERENE RAEIARRPDS NLPAHYQAFR SELAKALNVD ESELPFVAEL IQVKP EEAQ WRGAIERAVG SNRLRILVAP ESAQEALRWV NQRNNRLHVR LLEVKLPHSP ARFFDDGFTR KLLWKDHPWR EAVKAL LAE SDRHAVDSPE QLHDTPHAMT VQGLMSGKQR FYDKHDQKRL DEDWLTGFDN RDRLNFLAKE IATLQEQVKT ANAAFEF AK GEVGLLQNQA ASFQKIEQID FDSIDVPGAK SQLDALRERL ENLTRPDSDA SVAKAKLDEA QTIESELDKQ LRAANKVT C VLDTELTLAR AAERKAQQTA QQGMKEEERE LSASHFPVVT LEQLPDIRDL ERQHERGIQH EIERVKAELH RLNIELTKR MSEAKRVDTG ALVEAGADLD DIPVYLQRLQ ELTEEALPEK LNRFLDYLNR SSDDGVTQLL SHIEHEVLVI EERLNELNET MFRVDFQPD RYLRLDTKKV VHESLRTLEK AQRQLNAARF VDDNGESHYK ALQVLVAQLR DASERNRTLG AKALLDPRFR L EFAVSVMD RQSGNVIESR TGSQGGSGGE KEIIASYVLT ASLSYALSPA GSRYPLFGTI ILDEAFSRSS HAVAGRIIAA LR EFGLHAV FITPNKEMRL LRDHTRSAIV VHRRGQNSNM ASLSWEELER HYQRRGNAG

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Macromolecule #3: Circular plasmid DNA (1843-MER)

MacromoleculeName: Circular plasmid DNA (1843-MER) / type: dna / ID: 3
Details: Only a portion of the plasmid (pSG6085, 1843 bp) 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 ...Details: Only a portion of the plasmid (pSG6085, 1843 bp) 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: 2 / 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 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: 26586 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V4.6) / Number images used: 129606
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-9qxu:
JetABC DNA loaded state monomer (open)

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