+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16020 | |||||||||
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Title | E. coli Wadjet JetABC dimer of dimers | |||||||||
Map data | ||||||||||
Sample |
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Keywords | SMC complexes / bacterial immunity / defense system / DNA loop extrusion / Wadjet / JetABCD / DNA cleavage / plasmid restriction / mksBEFG / mobile genetic elements / horizontal gene transfer / eptABCD / mukBEF / DNA BINDING PROTEIN | |||||||||
Function / homology | Wadjet 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 species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 Å | |||||||||
Authors | Roisne-Hamelin F / Beckert B / Myasnikov A / Li Y / Gruber S | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Mol Cell / Year: 2022 Title: DNA-measuring Wadjet SMC ATPases restrict smaller circular plasmids by DNA cleavage. Authors: Hon Wing Liu / Florian Roisné-Hamelin / Bertrand Beckert / Yan Li / Alexander Myasnikov / Stephan Gruber / Abstract: Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC ...Structural maintenance of chromosome (SMC) complexes fold DNA by loop extrusion to support chromosome segregation and genome maintenance. Wadjet systems (JetABCD/MksBEFG/EptABCD) are derivative SMC complexes with roles in bacterial immunity against selfish DNA. Here, we show that JetABCD restricts circular plasmids with an upper size limit of about 100 kb, whereas a linear plasmid evades restriction. Purified JetABCD complexes cleave circular DNA molecules, regardless of the DNA helical topology; cleavage is DNA sequence nonspecific and depends on the SMC ATPase. A cryo-EM structure reveals a distinct JetABC dimer-of-dimers geometry, with the two SMC dimers facing in opposite direction-rather than the same as observed with MukBEF. We hypothesize that JetABCD is a DNA-shape-specific endonuclease and propose the "total extrusion model" for DNA cleavage exclusively when extrusion of an entire plasmid has been completed by a JetABCD complex. Total extrusion cannot be achieved on the larger chromosome, explaining how self-DNA may evade processing. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16020.map.gz | 16.1 MB | EMDB map data format | |
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Header (meta data) | emd-16020-v30.xml emd-16020.xml | 22.3 KB 22.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16020_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_16020.png | 91.9 KB | ||
Masks | emd_16020_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-16020.cif.gz | 6.8 KB | ||
Others | emd_16020_additional_1.map.gz emd_16020_additional_2.map.gz emd_16020_half_map_1.map.gz emd_16020_half_map_2.map.gz | 193.5 MB 226.6 MB 193.3 MB 193.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16020 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16020 | HTTPS FTP |
-Validation report
Summary document | emd_16020_validation.pdf.gz | 948.8 KB | Display | EMDB validaton report |
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Full document | emd_16020_full_validation.pdf.gz | 948.4 KB | Display | |
Data in XML | emd_16020_validation.xml.gz | 21.8 KB | Display | |
Data in CIF | emd_16020_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16020 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16020 | HTTPS FTP |
-Related structure data
Related structure data | 8bfnMC 8as8C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16020.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1616 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16020_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_16020_additional_1.map | ||||||||||||
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Density Histograms |
-Additional map: #2
File | emd_16020_additional_2.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_16020_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16020_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : JetABC(D)
Entire | Name: JetABC(D) |
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Components |
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-Supramolecule #1: JetABC(D)
Supramolecule | Name: JetABC(D) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: E. coli JetABCD was purified by gel filtration. Note that JetD is not visible in the map. |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: GF4-3 |
-Macromolecule #1: JetC
Macromolecule | Name: JetC / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 124.562938 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 UniProtKB: ATP synthase |
-Macromolecule #2: JetB
Macromolecule | Name: JetB / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 28.020416 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 UniProtKB: DUF4194 domain-containing protein |
-Macromolecule #3: JetA
Macromolecule | Name: JetA / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: GF4-3 |
Molecular weight | Theoretical: 63.350883 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 UniProtKB: DUF3375 family protein |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |