8H2H

Cryo-EM structure of a Group II Intron Complexed with its Reverse Transcriptase

• PDB DOI: https://doi.org/10.2210/pdb8H2H/pdb
• NAKB: 8H2H
• EM Map EMD-33039: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Lactococcus lactis
• Expression System: Lactococcus lactis
• Mutation(s): No 


• Deposited: 2022-10-06 Released: 2022-11-23 
• Deposition Author(s): Liu, N., Dong, X.L., Qu, G.S., Wang, J., Wang, H.W., Belfort, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Functionalized graphene grids with various charges for single-particle cryo-EM.

Lu, Y., Liu, N., Liu, Y., Zheng, L., Yang, J., Wang, J., Jia, X., Zi, Q., Peng, H., Rao, Y., Wang, H.W.

(2022) Nat Commun 13: 6718-6718

• PubMed: 36344519 
• DOI: https://doi.org/10.1038/s41467-022-34579-w
• Primary Citation of Related Structures:  
  8H2H


• PubMed 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 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.

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Organizational Affiliation: 

School of Life Sciences, Tsinghua University, Beijing, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 365.39 kDa 
• Atom Count: 20,016 
• Modelled Residue Count: 1,303 
• Deposited Residue Count: 1,513 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Group II intron-encoded protein LtrA	C [auth D]	599	Lactococcus lactis	Mutation(s): 0  Gene Names: ltrA, matR EC: 2.7.7.49 (PDB Primary Data), 3.1 (PDB Primary Data)
UniProt
Find proteins for P0A3U0 (Lactococcus lactis subsp. cremoris) Explore P0A3U0  Go to UniProtKB:  P0A3U0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
LtrB	A	902	Lactococcus lactis

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*AP*CP*AP*UP*CP*CP*AP*UP*AP*AP*C)-3')	B	12	Lactococcus lactis

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-11-23 
Deposition Author(s): Liu, N., Dong, X.L., Qu, G.S., Wang, J., Wang, H.W., Belfort, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-11-23
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Structure summary