[English] 日本語
Yorodumi
- EMDB-18136: ATP-bound IstB in complex to duplex DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18136
TitleATP-bound IstB in complex to duplex DNA
Map dataSharpened Map
Sample
  • Complex: IstB transposition regulator AAA+ ATPase bound to target DNA
    • Complex: Insertion sequence IS5376 putative ATP-binding protein
      • Protein or peptide: Insertion sequence IS5376 putative ATP-binding protein
    • Complex: DNA (48-MER) Target DNA FW and Rv
      • DNA: DNA (48-MER) Target DNA FW
      • DNA: DNA (48-MER) Traget DNA Rv
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDNA Transposition / transposon / transpososome / AAA+ ATPases / target DNA / IS21 / IstB / Insertion sequence / DNA BINDING PROTEIN / cryo-electron microscopy.
Function / homologyDNA replication protein DnaC/insertion sequence putative ATP-binding protein / IstB-like ATP-binding protein / IstB-like ATP binding protein / ClpA/B family / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Insertion sequence IS5376 putative ATP-binding protein
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
Authorsde la Gandara A / Spinola-Amilibia M / Araujo-Bazan L / Nunez-Ramirez R / Berger JM / Arias-Palomo E
Funding support Spain, 2 items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2020-120275GB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPRE2018-086026 Spain
CitationJournal: Nature / Year: 2024
Title: Molecular basis for transposase activation by a dedicated AAA+ ATPase.
Authors: Álvaro de la Gándara / Mercedes Spínola-Amilibia / Lidia Araújo-Bazán / Rafael Núñez-Ramírez / James M Berger / Ernesto Arias-Palomo /
Abstract: Transposases drive chromosomal rearrangements and the dissemination of drug-resistance genes and toxins. Although some transposases act alone, many rely on dedicated AAA+ ATPase subunits that ...Transposases drive chromosomal rearrangements and the dissemination of drug-resistance genes and toxins. Although some transposases act alone, many rely on dedicated AAA+ ATPase subunits that regulate site selectivity and catalytic function through poorly understood mechanisms. Using IS21 as a model transposase system, we show how an ATPase regulator uses nucleotide-controlled assembly and DNA deformation to enable structure-based site selectivity, transposase recruitment, and activation and integration. Solution and cryogenic electron microscopy studies show that the IstB ATPase self-assembles into an autoinhibited pentamer of dimers that tightly curves target DNA into a half-coil. Two of these decamers dimerize, which stabilizes the target nucleic acid into a kinked S-shaped configuration that engages the IstA transposase at the interface between the two IstB oligomers to form an approximately 1 MDa transpososome complex. Specific interactions stimulate regulator ATPase activity and trigger a large conformational change on the transposase that positions the catalytic site to perform DNA strand transfer. These studies help explain how AAA+ ATPase regulators-which are used by classical transposition systems such as Tn7, Mu and CRISPR-associated elements-can remodel their substrate DNA and cognate transposases to promote function.
History
DepositionAug 4, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18136.png

Downloads & links

-
Map

FileDownload / File: emd_18136.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened Map
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.21831192 - 0.2675998
Average (Standard dev.)-0.000008997276 (±0.0050750994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 305.27997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18136_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : IstB transposition regulator AAA+ ATPase bound to target DNA

EntireName: IstB transposition regulator AAA+ ATPase bound to target DNA
Components
  • Complex: IstB transposition regulator AAA+ ATPase bound to target DNA
    • Complex: Insertion sequence IS5376 putative ATP-binding protein
      • Protein or peptide: Insertion sequence IS5376 putative ATP-binding protein
    • Complex: DNA (48-MER) Target DNA FW and Rv
      • DNA: DNA (48-MER) Target DNA FW
      • DNA: DNA (48-MER) Traget DNA Rv
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: IstB transposition regulator AAA+ ATPase bound to target DNA

SupramoleculeName: IstB transposition regulator AAA+ ATPase bound to target DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Complex of IstB transposition regulator AAA+ ATPase bound to target DNA
Molecular weightTheoretical: 337 KDa

-
Supramolecule #2: Insertion sequence IS5376 putative ATP-binding protein

SupramoleculeName: Insertion sequence IS5376 putative ATP-binding protein
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)

-
Supramolecule #3: DNA (48-MER) Target DNA FW and Rv

SupramoleculeName: DNA (48-MER) Target DNA FW and Rv / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Geobacillus stearothermophilus (bacteria) / Synthetically produced: Yes

-
Macromolecule #1: Insertion sequence IS5376 putative ATP-binding protein

MacromoleculeName: Insertion sequence IS5376 putative ATP-binding protein
type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 29.602275 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPNMKERIHE YCHRLHLPVM AERWSAMAEY ASTHNISYSE FLFRLLEAEI VEKQARSIQT LIKLSKLPYR KTIDTFDFTA QPSVDERRI RELLTLSFID RKENILFLGP PGIGKTHLAI SIGMEAIARG YKTYFITAHD LVNQLRRADQ EGKLEKKLRV F VKPTVLII ...String:
GPNMKERIHE YCHRLHLPVM AERWSAMAEY ASTHNISYSE FLFRLLEAEI VEKQARSIQT LIKLSKLPYR KTIDTFDFTA QPSVDERRI RELLTLSFID RKENILFLGP PGIGKTHLAI SIGMEAIARG YKTYFITAHD LVNQLRRADQ EGKLEKKLRV F VKPTVLII DEMGYLKLDP NSAHYLFQVI ARRYEHAPII LTSNKSFGEW GEIVGDSVLA TAMLDRLLHH SIIFNLKGES YR LREKRLQ EEKQKDQ

UniProtKB: Insertion sequence IS5376 putative ATP-binding protein

-
Macromolecule #2: DNA (48-MER) Target DNA FW

MacromoleculeName: DNA (48-MER) Target DNA FW / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 18.401746 KDa
SequenceString: (DT)(DG)(DC)(DT)(DT)(DG)(DC)(DG)(DA)(DT) (DG)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DT) (DG)(DT)(DT)(DA)(DG)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DG)(DA)(DC)(DT)(DA)(DG)(DT) (DT) (DA)(DT)(DG)(DC)(DC)(DA) ...String:
(DT)(DG)(DC)(DT)(DT)(DG)(DC)(DG)(DA)(DT) (DG)(DA)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DT) (DG)(DT)(DT)(DA)(DG)(DC)(DC)(DA)(DC) (DG)(DC)(DT)(DG)(DA)(DC)(DT)(DA)(DG)(DT) (DT) (DA)(DT)(DG)(DC)(DC)(DA)(DT)(DG) (DC)(DC)(DT)(DC)(DC)(DC)(DT)(DT)(DC)(DA) (DG)(DG)

-
Macromolecule #3: DNA (48-MER) Traget DNA Rv

MacromoleculeName: DNA (48-MER) Traget DNA Rv / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 18.584918 KDa
SequenceString: (DC)(DC)(DT)(DG)(DA)(DA)(DG)(DG)(DG)(DA) (DG)(DG)(DC)(DA)(DT)(DG)(DG)(DC)(DA)(DT) (DA)(DA)(DC)(DT)(DA)(DG)(DT)(DC)(DA) (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DA) (DC) (DA)(DC)(DG)(DT)(DC)(DG) ...String:
(DC)(DC)(DT)(DG)(DA)(DA)(DG)(DG)(DG)(DA) (DG)(DG)(DC)(DA)(DT)(DG)(DG)(DC)(DA)(DT) (DA)(DA)(DC)(DT)(DA)(DG)(DT)(DC)(DA) (DG)(DC)(DG)(DT)(DG)(DG)(DC)(DT)(DA)(DA) (DC) (DA)(DC)(DG)(DT)(DC)(DG)(DG)(DA) (DT)(DC)(DA)(DT)(DC)(DG)(DC)(DA)(DA)(DG) (DC)(DA)

-
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 10 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClSodium chloride
5.0 mMMgCl2Magnesium chloride
1.0 mMDTT1,4-Dithiothreitol
1.0 mMATPAdenosine 5-triphosphate
0.015 %NP-40NP-40
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 5.0 sec. / Average electron dose: 60.0 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: 2.7 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

DetailsSuper-resolution counting mode
Particle selectionNumber selected: 2439865
Startup modelType of model: OTHER / Details: Obtained, from negative staining EM data
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 306745
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 6 / Avg.num./class: 230000 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 95.21
Output model

PDB-8q3w:
ATP-bound IstB in complex to duplex DNA

+
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