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Yorodumi- PDB-7lhl: cryo-EM structure of Mycobacterium smegmatis Lhr helicase C-termi... -
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-Basic information
Entry | Database: PDB / ID: 7lhl | |||||||||
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Title | cryo-EM structure of Mycobacterium smegmatis Lhr helicase C-terminal domain | |||||||||
Components | ATP-dependent DNA helicase | |||||||||
Keywords | HYDROLASE / helicase / winged helix | |||||||||
Function / homology | Function and homology information hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleic acid binding / RNA helicase activity / RNA helicase / ATP binding Similarity search - Function | |||||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Wang, J. / Warren, G.M. / Shuman, S. / Patel, D.J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nucleic Acids Res / Year: 2021 Title: Oligomeric quaternary structure of Escherichia coli and Mycobacterium smegmatis Lhr helicases is nucleated by a novel C-terminal domain composed of five winged-helix modules. Authors: Garrett M Warren / Juncheng Wang / Dinshaw J Patel / Stewart Shuman / Abstract: Mycobacterium smegmatis Lhr (MsmLhr; 1507-aa) is the founder of a novel clade of bacterial helicases. MsmLhr consists of an N-terminal helicase domain (aa 1-856) with a distinctive tertiary structure ...Mycobacterium smegmatis Lhr (MsmLhr; 1507-aa) is the founder of a novel clade of bacterial helicases. MsmLhr consists of an N-terminal helicase domain (aa 1-856) with a distinctive tertiary structure (Lhr-Core) and a C-terminal domain (Lhr-CTD) of unknown structure. Here, we report that Escherichia coli Lhr (EcoLhr; 1538-aa) is an ATPase, translocase and ATP-dependent helicase. Like MsmLhr, EcoLhr translocates 3' to 5' on ssDNA and unwinds secondary structures en route, with RNA:DNA hybrid being preferred versus DNA:DNA duplex. The ATPase and translocase activities of EcoLhr inhere to its 877-aa Core domain. Full-length EcoLhr and MsmLhr have homo-oligomeric quaternary structures in solution, whereas their respective Core domains are monomers. The MsmLhr CTD per se is a homo-oligomer in solution. We employed cryo-EM to solve the structure of the CTD of full-length MsmLhr. The CTD protomer is composed of a series of five winged-helix (WH) modules and a β-barrel module. The CTD adopts a unique homo-tetrameric quaternary structure. A Lhr-CTD subdomain, comprising three tandem WH modules and the β-barrel, is structurally homologous to AlkZ, a bacterial DNA glycosylase that recognizes and excises inter-strand DNA crosslinks. This homology is noteworthy given that Lhr is induced in mycobacteria exposed to the inter-strand crosslinker mitomycin C. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7lhl.cif.gz | 442.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lhl.ent.gz | 321.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lhl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lhl_validation.pdf.gz | 975.3 KB | Display | wwPDB validaton report |
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Full document | 7lhl_full_validation.pdf.gz | 1014.3 KB | Display | |
Data in XML | 7lhl_validation.xml.gz | 63.2 KB | Display | |
Data in CIF | 7lhl_validation.cif.gz | 96.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/7lhl ftp://data.pdbj.org/pub/pdb/validation_reports/lh/7lhl | HTTPS FTP |
-Related structure data
Related structure data | 23345MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 162009.562 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: lhr, ERS451418_01790 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0D6HFY2, RNA helicase |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Tetramer structure of ATP-dependent DNA helicase Lhr C-terminal domain Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 260 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Mycolicibacterium smegmatis (bacteria) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 22500 X / Calibrated magnification: 47262 X |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: RELION / Category: initial Euler assignment | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101323 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||
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