8H2H | pdb_00008h2h

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.
Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.
Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.
Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China.
School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. [e-mail].
Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China. [e-mail].
Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China.
School of Pharmaceutical Sciences, Tsinghua University, Beijing, China.
Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
Beijing Graphene Institute, Beijing, China.
College of Life Sciences, Wuhan University, Wuhan, Hubei, China.
Center for Nanochemistry, Beijing Science and Engineering Center for Nanocarbons, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China. [e-mail].
Beijing Graphene Institute, Beijing, China. [e-mail].
Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. [e-mail].
Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China. [e-mail].
Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, China. [e-mail].
School of Pharmaceutical Sciences, Tsinghua University, Beijing, China. [e-mail].
School of Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China. [e-mail].
Beijing Frontier Research Center for Biological Structures, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. [e-mail].
Ministry of Education Key Laboratory of Protein Sciences, Tsinghua University, Beijing, China. [e-mail].

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 
• Modeled 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