7WNU

Mycobacterium tuberculosis Rnase J complex with 7nt RNA

• PDB DOI: https://doi.org/10.2210/pdb7WNU/pdb
• NAKB: 7WNU

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Mycobacterium tuberculosis H37Rv, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-01-19 Released: 2023-01-25 
• Deposition Author(s): Li, J., Hu, J., Bao, L., Zhan, B., Li, Z.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Structural insights into RNase J that plays an essential role in Mycobacterium tuberculosis RNA metabolism

Bao, L., Hu, J., Zhan, B., Chi, M., Li, Z., Wang, S., Shan, C., Zhao, Z., Guo, Y., Ding, X., Ji, C., Tao, S., Ni, T., Zhang, X., Zhao, G., Li, J.

(2023) Nat Commun 14: 2280

• DOI: https://doi.org/10.1038/s41467-023-38045-z

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 123.98 kDa 
• Atom Count: 8,540 
• Modelled Residue Count: 1,120 
• Deposited Residue Count: 1,130 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J	A, B	558	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: rnj EC: 3.5.2.6 (PDB Primary Data), 3.1 (UniProt)
UniProt
Find proteins for P9WGZ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ9  Go to UniProtKB:  P9WGZ9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*AP*AP*AP*AP*AP*AP*A)-3')	C, D	7	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.06	α = 90
b = 145.38	β = 90
c = 192.1	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data scaling
PHENIX	phasing
HKL-3000	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Li, J., Hu, J., Bao, L., Zhan, B., Li, Z.

---

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0500600

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-09-04
  Changes: Database references