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- EMDB-23271: Helitron transposase bound to LTS -

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Basic information

Entry
Database: EMDB / ID: EMD-23271
TitleHelitron transposase bound to LTS
Map data
Sample
  • Complex: Helraiser complex with LTS
    • Protein or peptide: Helraiser K1068Q
    • DNA: LTS
  • Ligand: ZINC ION
KeywordsHelitron / transposase / evolution / gene editing / gene capture / rolling circle / replication / recombination / nuclease / helicase / relaxase
Biological speciessynthetic construct (others) / Myotis lucifugus (little brown bat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.66 Å
AuthorsKosek D / Dyda F
Funding support1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)
CitationJournal: Mol Cell / Year: 2021
Title: The large bat Helitron DNA transposase forms a compact monomeric assembly that buries and protects its covalently bound 5'-transposon end.
Authors: Dalibor Kosek / Ivana Grabundzija / Haotian Lei / Ilija Bilic / Huaibin Wang / Yukun Jin / Graham F Peaslee / Alison B Hickman / Fred Dyda /
Abstract: Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle ...Helitrons are widespread eukaryotic DNA transposons that have significantly contributed to genome variability and evolution, in part because of their distinctive, replicative rolling-circle mechanism, which often mobilizes adjacent genes. Although most eukaryotic transposases form oligomers and use RNase H-like domains to break and rejoin double-stranded DNA (dsDNA), Helitron transposases contain a single-stranded DNA (ssDNA)-specific HUH endonuclease domain. Here, we report the cryo-electron microscopy structure of a Helitron transposase bound to the 5'-transposon end, providing insight into its multidomain architecture and function. The monomeric transposase forms a tightly packed assembly that buries the covalently attached cleaved end, protecting it until the second end becomes available. The structure reveals unexpected architectural similarity to TraI, a bacterial relaxase that also catalyzes ssDNA movement. The HUH active site suggests how two juxtaposed tyrosines, a feature of many replication initiators that use HUH nucleases, couple the conformational shift of an α-helix to control strand cleavage and ligation reactions.
History
DepositionJan 10, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lcc
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23271.png

Downloads & links

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Map

FileDownload / File: emd_23271.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.08 Å/pix.
x 220 pix.
= 237.6 Å		1.08 Å/pix.
x 220 pix.
= 237.6 Å		1.08 Å/pix.
x 220 pix.
= 237.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.5 / Movie #1: 5
Minimum - Maximum-25.867163000000001 - 43.092410000000001
Average (Standard dev.)-0.000000000001898 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 237.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z237.600237.600237.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ220220220
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-25.86743.092-0.000

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Supplemental data

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Sample components

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Entire : Helraiser complex with LTS

EntireName: Helraiser complex with LTS
Components
  • Complex: Helraiser complex with LTS
    • Protein or peptide: Helraiser K1068Q
    • DNA: LTS
  • Ligand: ZINC ION

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Supramolecule #1: Helraiser complex with LTS

SupramoleculeName: Helraiser complex with LTS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 170 KDa

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Macromolecule #1: Helraiser K1068Q

MacromoleculeName: Helraiser K1068Q / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 171.253484 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSKEQLLIQR SSAAERCRRY RQKMSAEQRA SDLERRRRLQ QNVSEEQLLE KRRSEAEKQR RHRQKMSKDQ RAFEVERRRW RRQNMSREQ SSTSTTNTGR NCLLSKNGVH EDAILEHSCG GMTVRCEFCL SLNFSDEKPS DGKFTRCCSK GKVCPNDIHF P DYPAYLKR ...String:
MSKEQLLIQR SSAAERCRRY RQKMSAEQRA SDLERRRRLQ QNVSEEQLLE KRRSEAEKQR RHRQKMSKDQ RAFEVERRRW RRQNMSREQ SSTSTTNTGR NCLLSKNGVH EDAILEHSCG GMTVRCEFCL SLNFSDEKPS DGKFTRCCSK GKVCPNDIHF P DYPAYLKR LMTNEDSDSK NFMENIRSIN SSFAFASMGA NIASPSGYGP YCFRIHGQVY HRTGTLHPSD GVSRKFAQLY IL DTAEATS KRLAMPENQG CSERLMININ NLMHEINELT KSYKMLHEVE KEAQSEAAAK GIAPTEVTMA IKYDRNSDPG RYN SPRVTE VAVIFRNEDG EPPFERDLLI HCKPDPNNPN ATKMKQISIL FPTLDAMTYP ILFPHGEKGW GTDIALRLRD NSVI DNNTR QNVRTRVTQM QYYGFHLSVR DTFNPILNAG KLTQQFIVDS YSKMEANRIN FIKANQSKLR VEKYSGLMDY LKSRS ENDN VPIGKMIILP SSFEGSPRNM QQRYQDAMAI VTKYGKPDLF ITMTCNPKWA DITNNLQRWQ KVENRPDLVA RVFNIK LNA LLNDICKFHL FGKVIAKIHV IEFQKRGLPH AHILLILDSE SKLRSEDDID RIVKAEIPDE DQCPRLFQIV KSNMVHG PC GIQNPNSPCM ENGKCSKGYP KEFQNATIGN IDGYPKYKRR SGSTMSIGNK VVDNTWIVPY NPYLCLKYNC HINVEVCA S IKSVKYLFKY IYKGHDCANI QISEKNIINH DEVQDFIDSR YVSAPEAVWR LFAMRMHDQS HAITRLAIHL PNDQNLYFH TDDFAEVLDR AKRHNSTLMA WFLLNREDSD ARNYYYWEIP QHYVFNNSLW TKRRKGGNKV LGRLFTVSFR EPERYYLRLL LLHVKGAIS FEDLRTVGGV TYDTFHEAAK HRGLLLDDTI WKDTIDDAII LNMPKQLRQL FAYICVFGCP SAADKLWDEN K SHFIEDFC WKLHRREGAC VNCEMHALNE IQEVFTLHGM KCSHFKLPDY PLLMNANTCD QLYEQQQAEV LINSLNDEQL AA FQTITSA IEDQTVHPKC FFLDGPGGSG QTYLYKVLTH YIRGRGGTVL PTASTGIAAN LLLGGRTFHS QYKLPIPLNE TSI SRLDIK SEVAKTIKKA QLLIIDECTM ASSHAINAID RLLREIMNLN VAFGGKVLLL GGDFRQCLSI VPHAMRSAIV QTSL KYCNV WGCFRKLSLK TNMRSEDSAY SEWLVKLGDG KLDSSFHLGM DIIEIPHEMI CNGSIIEATF GNSISIDNIK NISKR AILC PKNEHVQKLN EEILDILDGD FHTYLSDDSI DSTDDAEKEN FPIEFLNSIT PSGMPCHKLK LKVGAIIMLL RNLNSK WGL CNGTRFIIKR LRPNIIEAEV LTGSAEGEVV LIPRIDLSPS DTGLPFKLIR RQFPVMPAFA MTINKSQGQT LDRVGIF LP EPVFAHGQLY VAFSRVRRAC DVKVKVVNTS SQGKLVKHSE SVFTLNVVYR EILE

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Macromolecule #2: LTS

MacromoleculeName: LTS / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Myotis lucifugus (little brown bat)
Molecular weightTheoretical: 6.158058 KDa
SequenceString:
(DT)(DC)(DC)(DT)(DA)(DT)(DA)(DT)(DA)(DA) (DT)(DA)(DA)(DA)(DA)(DG)(DA)(DG)(DA)(DA)

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.3 mg/mL
BufferpH: 7.4
GridModel: C-flat-1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Number grids imaged: 1 / Average electron dose: 73.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1982458
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 937125
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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Atomic model buiding 1

DetailsThe initial model has been traced manualy, then refined in Rosetta and finished in Coot 9.0
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7lcc:
Helitron transposase bound to LTS

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