9N9Q | pdb_00009n9q

Cryo-EM structure of the RNA-guided transcription complex

PDB DOI: https://doi.org/10.2210/pdb9N9Q/pdb
EM Map EMD-49176: EMDB EMDataResource

Classification: RNA BINDING PROTEIN/DNA/RNA
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

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

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

Renjian, X., Leifu, C.

To be published.

Macromolecule Content

Total Structure Weight: 597.98 kDa
Atom Count: 38,028
Modeled Residue Count: 4,446
Deposited Residue Count: 4,751
Unique protein chains: 6
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease-deactivated Cas12f	A, B	365	Flagellimonas taeanensis	Mutation(s): 0
Entity Groups
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RpoE	C	261	Flagellimonas taeanensis	Mutation(s): 0
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit alpha	D, E	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
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UniProt Group	A0A1M6YWR9
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	F	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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A3A1NXR2
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta'	G	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
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UniProt Group	A0A3A1NXQ1
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase Rpb6	H	108	Flagellimonas taeanensis	Mutation(s): 0 Gene Names: SAMN05216293_3853
UniProt
Find proteins for A0A1M7BX03 (Flagellimonas taeanensis) Explore A0A1M7BX03 Go to UniProtKB: A0A1M7BX03
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1M7BX03
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Length	Organism	Image
DNA non-template strand	I [auth a]	99	Flagellimonas taeanensis
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Length	Organism	Image
DNA template strand	J [auth b]	99	Flagellimonas taeanensis
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Length	Organism	Image
gRNA (85-MER)	K [auth c]	93	Flagellimonas taeanensis
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Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-12-24

Deposition Author(s):

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	--