8KDA

Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs

• PDB DOI: https://doi.org/10.2210/pdb8KDA/pdb
• EM Map EMD-37129: EMDB EMDataResource
• NAKB: 8KDA

• Classification: HYDROLASE/RNA
• Organism(s): Hydrogenobacter thermophilus TK-6, Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-08-09 Released: 2024-08-14 
• Deposition Author(s): Teramoto, T., Adachi, N., Yokogawa, T., Koyasu, T., Mayanagi, K., Nakamura, T., Senda, T., Kakuta, Y.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs

Teramoto, T., Koyasu, T., Yokogawa, T., Adachi, N., Mayanagi, K., Nakamura, T., Senda, T., Kakuta, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Helical - H  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 381.64 kDa 
• Atom Count: 26,222 
• Modelled Residue Count: 2,626 
• Deposited Residue Count: 2,633 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-free ribonuclease P	A [auth E], G [auth F], H [auth G], I [auth H], J [auth C], K [auth D], L [auth I], M [auth J], N [auth A], O [auth B], P [auth K], Q [auth L]	189	Hydrogenobacter thermophilus TK-6	Mutation(s): 0  Gene Names: HTH_1307 EC: 3.1.26.5
UniProt
Find proteins for D3DIV8 (Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)) Explore D3DIV8  Go to UniProtKB:  D3DIV8

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Aquifex aeolicus pre-tRNAVal	B [auth T], C [auth M], D [auth N], E [auth O], F [auth P]	73	Aquifex aeolicus

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	R [auth E], S [auth E], T [auth F], U [auth G], V [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.19 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	4

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Teramoto, T., Adachi, N., Yokogawa, T., Koyasu, T., Mayanagi, K., Nakamura, T., Senda, T., Kakuta, Y.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	21K06032
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101071
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101091

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release