[English] 日本語
Yorodumi
- EMDB-15344: Type V-K CAST TnsB bound to LTR-SR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15344
TitleType V-K CAST TnsB bound to LTR-SR
Map data
Sample
  • Complex: Type V-K CAST TnsB bound to LTR-SR
    • Protein or peptide: TnsB
    • DNA: RightElement
    • DNA: LeftElement
Biological speciesScytonema hofmannii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.2 Å
AuthorsTenjo-Castano F / Sofos N / Lopez-Mendez B / Stutzke LS / Fuglsang A / Stella S / Montoya G
Funding support Denmark, 4 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF0024386 Denmark
Novo Nordisk FoundationNNF14CC0001 Denmark
Novo Nordisk FoundationNNF17SA0030214 Denmark
Novo Nordisk FoundationNNF18OC0055061 Denmark
CitationJournal: Nat Commun / Year: 2022
Title: Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon.
Authors: Francisco Tenjo-Castaño / Nicholas Sofos / Blanca López-Méndez / Luisa S Stutzke / Anders Fuglsang / Stefano Stella / Guillermo Montoya /
Abstract: CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opted CRISPR-Cas systems for RNA-guided transposition. Here we present the 2.4 Å cryo-EM structure of the Scytonema ...CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opted CRISPR-Cas systems for RNA-guided transposition. Here we present the 2.4 Å cryo-EM structure of the Scytonema hofmannii (sh) TnsB transposase from Type V-K CAST, bound to the strand transfer DNA. The strand transfer complex displays an intertwined pseudo-symmetrical architecture. Two protomers involved in strand transfer display a catalytically competent active site composed by DDE residues, while other two, which play a key structural role, show active sites where the catalytic residues are not properly positioned for phosphodiester hydrolysis. Transposon end recognition is accomplished by the NTD1/2 helical domains. A singular in trans association of NTD1 domains of the catalytically competent subunits with the inactive DDE domains reinforces the assembly. Collectively, the structural features suggest that catalysis is coupled to protein-DNA assembly to secure proper DNA integration. DNA binding residue mutants reveal that lack of specificity decreases activity, but it could increase transposition in some cases. Our structure sheds light on the strand transfer reaction of DDE transposases and offers new insights into CAST transposition.
History
DepositionJul 5, 2022-
Header (metadata) releaseOct 19, 2022-
Map releaseOct 19, 2022-
UpdateOct 19, 2022-
Current statusOct 19, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15344.png

Downloads & links

-
Map

FileDownload / File: emd_15344.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.98 Å
Density
Contour LevelBy AUTHOR: 0.0504
Minimum - Maximum-0.13324593 - 0.46563247
Average (Standard dev.)-1.9994433e-05 (±0.013075983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 392.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_15344_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15344_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Type V-K CAST TnsB bound to LTR-SR

EntireName: Type V-K CAST TnsB bound to LTR-SR
Components
  • Complex: Type V-K CAST TnsB bound to LTR-SR
    • Protein or peptide: TnsB
    • DNA: RightElement
    • DNA: LeftElement

-
Supramolecule #1: Type V-K CAST TnsB bound to LTR-SR

SupramoleculeName: Type V-K CAST TnsB bound to LTR-SR / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Scytonema hofmannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 359 KDa

-
Macromolecule #1: TnsB

MacromoleculeName: TnsB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Scytonema hofmannii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSQQNPDLA VHPLAIPMEG LLGESATTLE KNVIATQLSE EAQVKLEVIQ SLLEPCDRTT YGQKLREAAE KLNVSLRTVQ RLVKNWEQDG LVGLTQTSRA DKGKHRIGEF WEN FITKTY KEGNKGSKRM TPKQVALRVE AKARELKDSK PPNYKTVLRV LAPILEKQQK ...String:
MNSQQNPDLA VHPLAIPMEG LLGESATTLE KNVIATQLSE EAQVKLEVIQ SLLEPCDRTT YGQKLREAAE KLNVSLRTVQ RLVKNWEQDG LVGLTQTSRA DKGKHRIGEF WEN FITKTY KEGNKGSKRM TPKQVALRVE AKARELKDSK PPNYKTVLRV LAPILEKQQK AKSIRSPGWR GTTLSVKTRE GKDLSVDYSN HVWQCDHTRV DVLLVDQHGE ILSRPWLT T VIDTYSRCIM GINLGFDAPS SGVVALALRH AILPKRYGSE YKLHCEWGTY GKPEHFYTDG GKDFRSNHLS QIGAQLGFVC HLRDRPSEGG VVERPFKTLN DQLFSTLPGY TGSN VQERP EDAEKDARLT LRELEQLLVR YIVDRYNQSI DARMGDQTRF ERWEAGLPTV PVPIPERDLD ICLMKQSRRT VQRGGCLQFQ NLMYRGEYLA GYAGETVNLR FDPRDITTI LVYRQENNQE VFLTRAHAQG LETEQLALDE AEAASRRLRT AGKTISNQSL LQEVVDRDAL VATKKSRKER QKLEQTVLRS AAVDESNRES LPSQIVEPDE VESTETVHSQ YEDIEVWDYE QLREEYGFGS EFELENLYFQ

-
Macromolecule #2: RightElement

MacromoleculeName: RightElement / type: dna / ID: 2 / Classification: DNA
Source (natural)Organism: Scytonema hofmannii (bacteria)
SequenceString: TGCTACGTCT CTACGTGTAC AGTGACTAAT TATATGTCGT TGTGACAAAT TATTGTCATC AGTAAAATCC TTATACAGTA TAGATTATAG CGCTTTGGCA GTTTTAGCAT AACCTCTTTG CAGTGACAAA ATAGATGTCG TTGTCCGTGA TTGTGACAAA TTAGCTGTCG ...String:
TGCTACGTCT CTACGTGTAC AGTGACTAAT TATATGTCGT TGTGACAAAT TATTGTCATC AGTAAAATCC TTATACAGTA TAGATTATAG CGCTTTGGCA GTTTTAGCAT AACCTCTTTG CAGTGACAAA ATAGATGTCG TTGTCCGTGA TTGTGACAAA TTAGCTGTCG CTTTGCAAGA TAGGAAAAAG CTTTTGTGTA TTTTCATAAT GACAAATTGA CTGTCGCAGG AGGTAA

-
Macromolecule #3: LeftElement

MacromoleculeName: LeftElement / type: dna / ID: 3 / Classification: DNA
Source (natural)Organism: Scytonema hofmannii (bacteria)
SequenceString:
ATTATATTGA TGACATTTAA TTTGTCATCA ATTAATTAAG CAACGCTGAT GGGTCACGAC GACAATTAAA TAGTCACAAT GACATTAATC TGTCACCGAC GACAGATAAT TTGTCACTGT ACACTACGCC TTTTGTGG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
300.0 mMNaClSodium chloridesodium chloride
50.0 mMHEPES2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid
5.0 mMMgCl2magnesium chloride
1.0 mMTCEPTris(2-carboxyethyl)phosphine
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 150000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 738 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2

-
Image processing

Particle selectionNumber selected: 38871
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2)
Startup modelType of model: NONE
Details: Ab initio reconstruction in cryoSPARC from the same data.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 11.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 5554

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

+
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://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