[English] 日本語
Yorodumi
- EMDB-27481: CryoEM structure of Pseudomonas aeruginosa PA14 JetABC in an uncl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-27481
TitleCryoEM structure of Pseudomonas aeruginosa PA14 JetABC in an unclamped state trapped in ATP dependent dimeric form
Map data
Sample
  • Complex: Reconstituted JetABC complex in the presence of DNA and ATP gamma S.
    • Protein or peptide: JetA
    • Protein or peptide: JetC
    • Protein or peptide: JetB
    • DNA: DNA (26-MER)
    • DNA: DNA (26-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsWadjet / Bacterial defense systems / JetA / JetB / JetC / Anti-plasmid defense system / EptA / EptB / EptC / MksB / MksE / MksF / SMC / DNA BINDING PROTEIN-DNA complex
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 / DUF3375 domain-containing protein / DUF4194 domain-containing protein / ATP synthase
Function and homology information
Biological speciesPseudomonas aeruginosa PA14 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsDeep A / Gu Y / Gao Y / Ego K / Herzik M / Zhou H / Corbett K
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 GM104141 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI148814 United States
CitationJournal: Mol Cell / Year: 2022
Title: The SMC-family Wadjet complex protects bacteria from plasmid transformation by recognition and cleavage of closed-circular DNA.
Authors: Amar Deep / Yajie Gu / Yong-Qi Gao / Kaori M Ego / Mark A Herzik / Huilin Zhou / Kevin D Corbett /
Abstract: Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through ...Self versus non-self discrimination is a key element of innate and adaptive immunity across life. In bacteria, CRISPR-Cas and restriction-modification systems recognize non-self nucleic acids through their sequence and their methylation state, respectively. Here, we show that the Wadjet defense system recognizes DNA topology to protect its host against plasmid transformation. By combining cryoelectron microscopy with cross-linking mass spectrometry, we show that Wadjet forms a complex similar to the bacterial condensin complex MukBEF, with a novel nuclease subunit similar to a type II DNA topoisomerase. Wadjet specifically cleaves closed-circular DNA in a reaction requiring ATP hydrolysis by the structural maintenance of chromosome (SMC) ATPase subunit JetC, suggesting that the complex could use DNA loop extrusion to sense its substrate's topology, then specifically activate the nuclease subunit JetD to cleave plasmid DNA. Overall, our data reveal how bacteria have co-opted a DNA maintenance machine to specifically recognize and destroy foreign DNAs through topology sensing.
History
DepositionJul 1, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_27481.png

Downloads & links

-
Map

FileDownload / File: emd_27481.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.4667 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.38171884 - 1.184534
Average (Standard dev.)-0.00064719055 (±0.019854603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 563.21277 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: half map for focused refinement of JetC and DNA.

Fileemd_27481_additional_1.map
Annotationhalf map for focused refinement of JetC and DNA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: half map for focused refinement of JetC and DNA.

Fileemd_27481_additional_2.map
Annotationhalf map for focused refinement of JetC and DNA.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: focused refinement of JetC and DNA, from over 170k particles.

Fileemd_27481_additional_3.map
Annotationfocused refinement of JetC and DNA, from over 170k particles.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_27481_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_27481_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Reconstituted JetABC complex in the presence of DNA and ATP gamma S.

EntireName: Reconstituted JetABC complex in the presence of DNA and ATP gamma S.
Components
  • Complex: Reconstituted JetABC complex in the presence of DNA and ATP gamma S.
    • Protein or peptide: JetA
    • Protein or peptide: JetC
    • Protein or peptide: JetB
    • DNA: DNA (26-MER)
    • DNA: DNA (26-MER)
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

-
Supramolecule #1: Reconstituted JetABC complex in the presence of DNA and ATP gamma S.

SupramoleculeName: Reconstituted JetABC complex in the presence of DNA and ATP gamma S.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Molecular weightTheoretical: 481 KDa

-
Macromolecule #1: JetA

MacromoleculeName: JetA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Molecular weightTheoretical: 59.2335 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAE ESAQQRSERY VSARSQHPAW LLLASRRAPL VLGCLRTLFE RAHDGIPMED ALQALSEMLA AYASQELYE IDPDATHLQA GRELREWIKR RLVVEREGRI YATDALESAI QFVDSLDSRI MTSTASRLSV VQREIENLET G LNPSPTGR ...String:
MKSSHHHHHH ENLYFQSNAE ESAQQRSERY VSARSQHPAW LLLASRRAPL VLGCLRTLFE RAHDGIPMED ALQALSEMLA AYASQELYE IDPDATHLQA GRELREWIKR RLVVEREGRI YATDALESAI QFVDSLDSRI MTSTASRLSV VQREIENLET G LNPSPTGR IASLRRRIQD LEHELARVEA GHVDVLDEAQ AIEGMREVYN LATSLRADFR RVEDSWREAD RALRHSIISE QS HRGEIVD RLLDGQDALL NTPEGRVFES FQQQLRQSAE LEVMRERLRT ILRHPAVPKA LNRPQQRELR WLALRLVRES QAV LQARAR SERDVRGFMK TGLAAEHHRV GQLLNDFFNL ALSVDWQRQS ERRKPACLPP VGVAITGVPA IERLRFKTLD DDDA GELDL SLKPAGLEQI DDDFWDAFDG LDREALIHDT LAVLVEQGRP VSLGELASLL PPAHDLETFA LWLAMAREAG IEVLT EERQ FVELVDEDEQ RWGFNLPYVG LDHEALKDID WEL

UniProtKB: DUF3375 domain-containing protein

-
Macromolecule #2: JetC

MacromoleculeName: JetC / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Molecular weightTheoretical: 126.68318 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSSHHHHHH ENLYFQSNAK QALLWRDSET FILTSIELYN WGGFQGYHRA EIDPSGTAVI GPTGSGKTTL VDALMTLLCA NPRYNLAST GGHESDRDLV SYVRGVTGPG DGGVEQSHIA RQGKTVTAIA ATLERDGAQV RLGAVLWFEG TSSSASDLKK L WLLSESPE ...String:
MKSSHHHHHH ENLYFQSNAK QALLWRDSET FILTSIELYN WGGFQGYHRA EIDPSGTAVI GPTGSGKTTL VDALMTLLCA NPRYNLAST GGHESDRDLV SYVRGVTGPG DGGVEQSHIA RQGKTVTAIA ATLERDGAQV RLGAVLWFEG TSSSASDLKK L WLLSESPE QTLEHWLSQH HAGGMRALRQ MEKDGMGIWP YPSKKAFLAR LRDYFEVGEN AFTLLNRAAG LKQLNSIDEI FR ELVLDDR SAFERAAEVA SSFDDLTDIH RELETARKQQ RSLQPVADGW ERYRALQEQL QDKQALEGIL PVWFAEQGYR LWL AETNRL EKEHKQAELD QAQCRSQLEI QKGVVDQHRQ RYLRVGGAGI DQLRGRIADW VRECDKRRLK AEQYQRLAKG LGLA DELSA AALEENQQQI AARLEILAQQ TTDARQKAFD AGLVQQELNG RLQSLQQERA EVERRPGSNL PGHFHAFRGD LAQEL GVDE SALPFVAELV QVKPEELAWR GAIERAIGSH RLRILVPQGS SQAALRWVNQ RHNRLHVRLL EVKEPSSRPV FFDDGF TRK LTFKEHPYRE AVKALLADND RHCVESTEQL RHTPHAMTAQ GLMSGKERFF DKQDQKRLDE DWLTGFDNRD RLAFLAE QI REVNEQLVPA KLALDAAQGD VGQLESQASL LQRIEELQFD DIDRPGAERQ LQSLRTQLDT LTRPDSNLAV IKAELDQA E ALRESLDQQL QRLIEQCVQL KTQFDQAASA TRKAYRGAEK GLSDTQRELA QAHFPILSTD DLGDIDELER KHTRELQGQ LKTLGEKLGD QKTELAKRMS DALKADTGAL AEVGRELVDV PRYLERLRVL TEEALPEKLK RFLEYLNRSS DDGVTQLLSY IDHEVSMIE ERLDDLNSTM QRVDFQPGRY LRLVAKKVIH ESLRTLQHAQ RQLNSARFID DEGESHYKAL QALVGLLKDA C EHSRNQGA KALLDPRFRL EFAVSVIDRE GNNLIETRTG SQGGSGGEKE IIASYVLTAS LSYALCPDGS SRPLFGTIVL DQ AFSRSSH AVAGRIIAAL REFGLHAVFI TPNKEMRLLR HHTRSAVVVH RRGVESSLVS LSWEALDEHH QQRIRAMHEV AH

UniProtKB: ATP synthase

-
Macromolecule #3: JetB

MacromoleculeName: JetB / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PA14 (bacteria)
Molecular weightTheoretical: 27.537037 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAGIFDRIAG ASGADETELT AEPMALDDGM DGEQPAMSAN IQVDERRTPQ RVREAVQEML KYGLLEESHK PNLYRSALTN IEVVDRILE PLDLAMGVDE VRGLVFVTVR QGEVAEQDDW SHPLVRRQRL NLEQSLLIAI LRQHFIAYEQ ESGTGASQAL V AVDELIPQ ...String:
MAGIFDRIAG ASGADETELT AEPMALDDGM DGEQPAMSAN IQVDERRTPQ RVREAVQEML KYGLLEESHK PNLYRSALTN IEVVDRILE PLDLAMGVDE VRGLVFVTVR QGEVAEQDDW SHPLVRRQRL NLEQSLLIAI LRQHFIAYEQ ESGTGASQAL V AVDELIPQ LQVYLGELGS EAKERNRIIT LLDQLKGHGL VSALDAHDRV IIRPIITHLA NPENLQALVV WLREQVEGAV TP AAGGEED EA

UniProtKB: DUF4194 domain-containing protein

-
Macromolecule #4: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 4
Details: Below mentioned hybridized oligonucleotides were used in the sample preparation. Considering the DNA binding is purely based on the electrostatic charge: polyA/polyT chain was used to ...Details: Below mentioned hybridized oligonucleotides were used in the sample preparation. Considering the DNA binding is purely based on the electrostatic charge: polyA/polyT chain was used to generate the model. JetABC_cryo_Fwd: GTGATAGTTAGAAACGTAATTGACTATAAAGATGATGACGATAAGTAGGATGTCTATAGACCAGG JetABC_cryo_Rev: CCTGGTCTATAGACATCCTACTTATCGTCATCATCTTTATAGTCAATTACGTTTCTAACTATCAC
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.864056 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)

-
Macromolecule #5: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 5
Details: Below mentioned hybridized oligonucleotides were used in the sample preparation. Considering the DNA binding is purely based on the electrostatic charge: polyA/polyT chain was used to ...Details: Below mentioned hybridized oligonucleotides were used in the sample preparation. Considering the DNA binding is purely based on the electrostatic charge: polyA/polyT chain was used to generate the model. JetABC_cryo_Fwd: GTGATAGTTAGAAACGTAATTGACTATAAAGATGATGACGATAAGTAGGATGTCTATAGACCAGG JetABC_cryo_Rev: CCTGGTCTATAGACATCCTACTTATCGTCATCATCTTTATAGTCAATTACGTTTCTAACTATCAC
Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.098421 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)

-
Macromolecule #6: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

-
Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
60.0 mMNaClSodium Chloride
30.0 mMC4H11NO3tris(hydroxymethyl)aminomethane
1.0 mMC9H16ClO6PTCEP
1.0 mMC10H16N5O12P3SATP gamma S
2.0 mMMgCl2Magnesium Chloride

Details: Prepared using deionized water and filtered sterilized.
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56600
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8dk2:
CryoEM structure of Pseudomonas aeruginosa PA14 JetABC in an unclamped state trapped in ATP dependent dimeric form

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more