9DVT | pdb_00009dvt

Cryo-EM structure of RpaA bound to PkaiBC DNA and the CTD of the alpha subunit of RNAP from the cyanobacterium Synechococcus elongatus

• PDB DOI: https://doi.org/10.2210/pdb9DVT/pdb
• EM Map EMD-47222: EMDB EMDataResource
• NAKB: 9DVT

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): synthetic construct, Synechococcus elongatus, Synechococcus elongatus PCC 7942 = FACHB-805
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-08 Released: 2025-10-15 
• Deposition Author(s): Fang, M., Gu, Y., Matyszewski, M., Leanca, M., LiWang, A., Yuzenkova, Y., Corbett, K.D., Golden, S.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.74 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico

Literature

Reconstitution of Circadian Transcription in vitro through RpaA Regulation

Fang, M., Gu, Y., Leanca, M., Matyszewski, M., LiWang, A., Yuzenkova, Y., Corbett, K.D., Golden, S.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 201.54 kDa 
• Atom Count: 6,369 
• Modeled Residue Count: 679 
• Deposited Residue Count: 1,416 
• Unique protein chains: 3
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	C [auth A]	309	Synechococcus elongatus	Mutation(s): 0  Gene Names: rpoA, Synpcc7942_2209 EC: 2.7.7.6
UniProt
Find proteins for Q31L30 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31L30  Go to UniProtKB:  Q31L30

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding dual master transcriptional regulator RpaA	D [auth R], E [auth S]	249	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0  Gene Names: rpaA, Synpcc7942_0095
UniProt
Find proteins for Q31S42 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31S42  Go to UniProtKB:  Q31S42

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA1	F [auth G]	399	Synechococcus elongatus PCC 7942 = FACHB-805	Mutation(s): 0  Gene Names: sigA1, rpoD1, Synpcc7942_0649
UniProt
Find proteins for P38023 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P38023  Go to UniProtKB:  P38023

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Non-template DNA	A [auth 1]	105	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Template DNA	B [auth 2]	105	synthetic construct

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PHD	D [auth R], E [auth S]	L-PEPTIDE LINKING	C4 H8 N O7 P		ASP

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.74 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: 2025-10-15 
Deposition Author(s): Fang, M., Gu, Y., Matyszewski, M., Leanca, M., LiWang, A., Yuzenkova, Y., Corbett, K.D., Golden, S.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM144121
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118290
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/W017385/1

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release