9N9P | pdb_00009n9p

Cryo-EM structure of the Fta RNAP complex

• PDB DOI: https://doi.org/10.2210/pdb9N9P/pdb
• EM Map EMD-49175: EMDB EMDataResource

• Classification: RNA BINDING PROTEIN
• Organism(s): Flagellimonas taeanensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2025-02-11 Released: 2025-12-24 
• Deposition Author(s): Chang, L., Sternberg, S.H., Xiao, R., Hoffmann, F.T., Wiegand, T., Xie, D.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), The Pew Charitable Trusts

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis of RNA-guided transcription via Cas12f-Sigma factor association

Renjian, X., Leifu, C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 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.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 390.14 kDa 
• Atom Count: 23,175 
• Modeled Residue Count: 2,933 
• Deposited Residue Count: 3,469 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	A, B	330	Flagellimonas taeanensis	Mutation(s): 0  Gene Names: rpoA, SAMN05216293_2985 EC: 2.7.7.6
UniProt
Find proteins for A0A1M6YWR9 (Flagellimonas taeanensis) Explore A0A1M6YWR9  Go to UniProtKB:  A0A1M6YWR9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	C	1,269	Flagellimonas taeanensis	Mutation(s): 0  Gene Names: rpoB, SAMN05216293_2127 EC: 2.7.7.6
UniProt
Find proteins for A0A3A1NXR2 (Flagellimonas taeanensis) Explore A0A3A1NXR2  Go to UniProtKB:  A0A3A1NXR2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	D	1,432	Flagellimonas taeanensis	Mutation(s): 0  Gene Names: rpoC, SAMN05216293_2128 EC: 2.7.7.6
UniProt
Find proteins for A0A3A1NXQ1 (Flagellimonas taeanensis) Explore A0A3A1NXQ1  Go to UniProtKB:  A0A3A1NXQ1

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase Rpb6	E	108	Flagellimonas taeanensis	Mutation(s): 0  Gene Names: SAMN05216293_3853
UniProt
Find proteins for A0A1M7BX03 (Flagellimonas taeanensis) Explore A0A1M7BX03  Go to UniProtKB:  A0A1M7BX03

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-24 
Deposition Author(s): Chang, L., Sternberg, S.H., Xiao, R., Hoffmann, F.T., Wiegand, T., Xie, D.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM138675
National Science Foundation (NSF, United States)	United States	2339799
National Science Foundation (NSF, United States)	United States	2239685
The Pew Charitable Trusts	United States	--

Revision History  

• Version 1.0: 2025-12-24
  Type: Initial release