9L6O | pdb_00009l6o

CryoEM structure of class Ib Ribonucleotide reductase from Mycobacterium thermoresistibile, conformer D

• PDB DOI: https://doi.org/10.2210/pdb9L6O/pdb
• EM Map EMD-62860: EMDB EMDataResource

• Classification: REPLICATION
• Organism(s): Mycolicibacterium thermoresistibile ATCC 19527
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-24 Released: 2026-07-01 
• Deposition Author(s): Yadav, L.R., Mande, S.C., Vinothkumar, K.R., Kumar, J.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Dynamics of Class Ib ribonucleotide reductase complex revealed by CryoEM

Yadav, L.R., Mande, S.C., Vinothkumar, K.R., Kumar, J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

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

Macromolecule Content 

• Total Structure Weight: 226.3 kDa 
• Atom Count: 14,848 
• Modeled Residue Count: 1,842 
• Deposited Residue Count: 1,970 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase subunit beta	A, C [auth B]	318	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: nrdF, KEK_07147 EC: 1.17.4.1
UniProt
Find proteins for P9WH71 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WH71  Go to UniProtKB:  P9WH71

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonucleoside-diphosphate reductase	B [auth F], D [auth E]	667	Mycolicibacterium thermoresistibile ATCC 19527	Mutation(s): 0  Gene Names: KEK_07092 EC: 1.17.4.1
UniProt
Find proteins for P9WH75 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WH75  Go to UniProtKB:  P9WH75

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	E [auth A], F [auth A], G [auth B], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	v3.3.2
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-07-01 
Deposition Author(s): Yadav, L.R., Mande, S.C., Vinothkumar, K.R., Kumar, J.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	Centre of Excellence Grant (BT/PR15450/COE/34/46/2016)
Department of Biotechnology (DBT, India)	India	DBT/PR12422/MED/31/287/2014

Revision History  

• Version 1.0: 2026-07-01
  Type: Initial release