9DVU | pdb_00009dvu

CryoEM structure of RpaA bound to PkaiBC DNA and Syn7942 RNAP-SigA holoenzyme

PDB DOI: https://doi.org/10.2210/pdb9DVU/pdb
EM Map EMD-47223: EMDB EMDataResource
NAKB: 9DVU

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 582.78 kDa
Atom Count: 35,249
Modeled Residue Count: 4,305
Deposited Residue Count: 4,843
Unique protein chains: 7
Unique nucleic acid chains: 2

Macromolecules

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	C [auth A], D [auth B]	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q31L30
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	E [auth C]	1,100	Synechococcus elongatus	Mutation(s): 0 Gene Names: rpoB, Synpcc7942_1522 EC: 2.7.7.6
UniProt
Find proteins for Q31N17 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31N17 Go to UniProtKB: Q31N17
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q31N17
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit gamma	F [auth D]	624	Synechococcus elongatus	Mutation(s): 0 Gene Names: rpoC1, Synpcc7942_1523 EC: 2.7.7.6
UniProt
Find proteins for P42079 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore P42079 Go to UniProtKB: P42079
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42079
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit omega	G [auth E]	76	Synechococcus elongatus	Mutation(s): 0 Gene Names: rpoZ, Synpcc7942_1710 EC: 2.7.7.6
UniProt
Find proteins for Q31MH9 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31MH9 Go to UniProtKB: Q31MH9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q31MH9
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	H [auth F]	1,318	Synechococcus elongatus	Mutation(s): 0 Gene Names: rpoC2, Synpcc7942_1524 EC: 2.7.7.6
UniProt
Find proteins for Q31N15 (Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)) Explore Q31N15 Go to UniProtKB: Q31N15
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q31N15
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase sigma factor SigA1	I [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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38023
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding dual master transcriptional regulator RpaA	J [auth R], K [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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q31S42
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Reference Sequence

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

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain N [auth F] MOL2 format, chain M [auth D] MOL2 format, chain N [auth F] mmCIF format, chain M [auth D] mmCIF format, chain N [auth F]	M [auth D], N [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth F] Interactions & Density Focus chain M [auth D] Focus chain N [auth F]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

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