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- EMDB-15609: E. coli Wadjet JetABC monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-15609
TitleE. coli Wadjet JetABC monomer
Map data
Sample
  • Complex: JetABC(D)
    • Protein or peptide: JetC
    • Protein or peptide: JetB
    • Protein or peptide: JetA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homologyWadjet protein JetB / Domain of unknown function (DUF4194) / Protein of unknown function DUF3375 / Protein of unknown function (DUF3375) / P-loop containing nucleoside triphosphate hydrolase / DUF4194 domain-containing protein / ATP synthase / DUF3375 family protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsRoisne-Hamelin F / Beckert B / Li Y / Myasnikov A / Gruber S
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)724482European Union
CitationJournal: Molecular Cell / Year: 2022
Title: DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage.
Authors: Liu HW / Roisne-Hamelin F / Beckert B / Li Y / Myasnikov A / Gruber S
History
DepositionAug 18, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15609.png

Downloads & links

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Map

FileDownload / File: emd_15609.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 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: 0.00183
Minimum - Maximum-0.017345754 - 0.03247221
Average (Standard dev.)3.7040486e-06 (±0.0004111319)
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_15609_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_15609_additional_1.map
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Half map: #2

Fileemd_15609_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_15609_half_map_2.map
Projections & Slices
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Sample components

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Entire : JetABC(D)

EntireName: JetABC(D)
Components
  • Complex: JetABC(D)
    • Protein or peptide: JetC
    • Protein or peptide: JetB
    • Protein or peptide: JetA
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: JetABC(D)

SupramoleculeName: JetABC(D) / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Details: E. coli JetABCD was purified by gel filtration. Note that JetD is not visible in the map.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3

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Macromolecule #1: JetC

MacromoleculeName: JetC / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 124.562938 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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 #2: JetB

MacromoleculeName: JetB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 28.020416 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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 #3: JetA

MacromoleculeName: JetA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: GF4-3
Molecular weightTheoretical: 63.350883 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAHHHHHHHH HHGGSSAWSH PQFEKGGGSG GGSGGGSWSH PQFEKLEVLF QGPAAMEENT RQRTENYISA KNQHPAWILL ATRRAPLVL SCLKTLFEKS HDGIPLEEAI QSLSSILIEH VSQEQYDINQ DNPFLQASRE LREWIKRRLI VERDGRIFAT D ALEVAITF ...String:
MAHHHHHHHH HHGGSSAWSH PQFEKGGGSG GGSGGGSWSH PQFEKLEVLF QGPAAMEENT RQRTENYISA KNQHPAWILL ATRRAPLVL SCLKTLFEKS HDGIPLEEAI QSLSSILIEH VSQEQYDINQ DNPFLQASRE LREWIKRRLI VERDGRIFAT D ALEVAITF VESLDNRFMT STASRLSTVQ REIENLETRL NPNPANRVAT LRRRISELER ELQEAEAGHI EVLETHQAVE HI RDVYNLA SSLRADFRRV EDSWREADRA LRQSIIGEQY HRGDIVERLL NDQDALLNTP EGRVFDSFQQ QLRQSSELKA MSE RLRVIL SHPSASDALN RLQRHDLRWL VKRLVDESQT VLQARARSER DVRGFMKTGL AAEHHRVGHL LNEFLNLALK LDWQ RQMIR KQEVPLPAVG VAVTGIPAIE RLRFKEVDDE AEQTLDLSNH AADLTQIGDD FWDAFNGLDR EVLIQQTLQL LAKEN RPVG LAELAELLPP AHDLETFAVW IGMAREAGIE VIDSQREFAE LSDGEGRRWR FNLPTTGLES QALMDIDWEG

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / 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) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124689
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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