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Yorodumi- PDB-8h2h: Cryo-EM structure of a Group II Intron Complexed with its Reverse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8h2h | ||||||
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Title | Cryo-EM structure of a Group II Intron Complexed with its Reverse Transcriptase | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / intron / RNA BINDING PROTEIN-RNA COMPLEX | ||||||
Function / homology | Function and homology information intron homing / mRNA processing / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / endonuclease activity / Hydrolases; Acting on ester bonds Similarity search - Function | ||||||
Biological species | Lactococcus lactis (lactic acid bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Liu, N. / Dong, X.L. / Qu, G.S. / Wang, J. / Wang, H.W. / Belfort, M. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Functionalized graphene grids with various charges for single-particle cryo-EM. Authors: Ye Lu / Nan Liu / Yongbo Liu / Liming Zheng / Junhao Yang / Jia Wang / Xia Jia / Qinru Zi / Hailin Peng / Yu Rao / Hong-Wei Wang / Abstract: A major hurdle for single particle cryo-EM in structural determination lies in the specimen preparation impaired by the air-water interface (AWI) and preferential particle-orientation problems. In ...A major hurdle for single particle cryo-EM in structural determination lies in the specimen preparation impaired by the air-water interface (AWI) and preferential particle-orientation problems. In this work, we develop functionalized graphene grids with various charges via a dediazoniation reaction for cryo-EM specimen preparation. The graphene grids are paraffin-assistant fabricated, which appear with less contaminations compared with those produced by polymer transfer method. By applying onto three different types of macromolecules, we demonstrate that the high-yield charged graphene grids bring macromolecules away from the AWI and enable adjustable particle-orientation distribution for more robust single particle cryo-EM structural determination. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8h2h.cif.gz | 484.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8h2h.ent.gz | 345 KB | Display | PDB format |
PDBx/mmJSON format | 8h2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h2/8h2h ftp://data.pdbj.org/pub/pdb/validation_reports/h2/8h2h | HTTPS FTP |
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-Related structure data
Related structure data | M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: RNA chain | Mass: 291363.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Production host: Lactococcus lactis (lactic acid bacteria) |
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#2: RNA chain | Mass: 3739.312 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Production host: Lactococcus lactis (lactic acid bacteria) |
#3: Protein | Mass: 70286.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactococcus lactis (lactic acid bacteria) Gene: ltrA, matR / Production host: Lactococcus lactis (lactic acid bacteria) References: UniProt: P0A3U0, RNA-directed DNA polymerase, Hydrolases; Acting on ester bonds |
-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: a Group II Intron Complexed with its Reverse Transcriptase Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Lactococcus lactis (lactic acid bacteria) |
Source (recombinant) | Organism: Lactococcus lactis (lactic acid bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 399660 / Symmetry type: POINT |