9JI3 | pdb_00009ji3

Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with two PhoP molecules

• PDB DOI: https://doi.org/10.2210/pdb9JI3/pdb
• NAKB: 9JI3
• EM Map EMD-61493: EMDB EMDataResource

• Classification: GENE REGULATION
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-11 Released: 2025-09-17 
• Deposition Author(s): Lin, W., Feng, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Mycobacterium tuberculosis transcription activation complex with two PhoP molecules

Lin, W., Feng, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C1D1E1F1 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 - A2 

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

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 524.51 kDa 
• Atom Count: 28,870 
• Modeled Residue Count: 3,549 
• Deposited Residue Count: 4,472 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	347	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rpoA EC: 2.7.7.6
UniProt
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ1  Go to UniProtKB:  P9WGZ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,178	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rpoB EC: 2.7.7.6
UniProt
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY9  Go to UniProtKB:  P9WGY9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,316	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rpoC EC: 2.7.7.6
UniProt
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY7  Go to UniProtKB:  P9WGY7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	E	110	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: rpoZ EC: 2.7.7.6
UniProt
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGY5  Go to UniProtKB:  P9WGY5

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA	H [auth F]	528	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: sigA
UniProt
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGI1  Go to UniProtKB:  P9WGI1

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding response regulator	I [auth J], J [auth K]	247	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: phoP
UniProt
Find proteins for P71814 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P71814  Go to UniProtKB:  P71814

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Non-template strand DNA	F [auth H]	76	Mycobacterium tuberculosis

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Template strand DNA	G	76	Mycobacterium tuberculosis

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	K [auth D], L [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.36 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-17 
Deposition Author(s): Lin, W., Feng, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-09-17
  Type: Initial release