9LQ8 | pdb_00009lq8

Cryo-EM structure of CTR-bound type III-B CRISPR-Cas effector complex

• PDB DOI: https://doi.org/10.2210/pdb9LQ8/pdb
• EM Map EMD-63296: EMDB EMDataResource
• NAKB: 9LQ8

• Classification: IMMUNE SYSTEM/RNA
• Organism(s): Bacteroides fragilis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-01-28 Released: 2025-11-26 
• Deposition Author(s): Jin, X., Duan, B., Chen, Z., Zhao, B.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Mechanisms of SAM-AMP synthesis and degradation in antiviral type III CRISPR signaling.

Duan, B., Jin, X., Chen, Z., Zhao, B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A3B2C1D1E1F1 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 367.14 kDa 
• Atom Count: 24,511 
• Modeled Residue Count: 2,903 
• Deposited Residue Count: 3,013 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cmr1	A	469	Bacteroides fragilis	Mutation(s): 0  Gene Names: F2Z89_11915, F3B44_04900, NXW39_14635
UniProt
Find proteins for A0A5M5QTL0 (Bacteroides fragilis) Explore A0A5M5QTL0  Go to UniProtKB:  A0A5M5QTL0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated protein Cmr3	B [auth C]	423	Bacteroides fragilis	Mutation(s): 0  Gene Names: NXW39_14645
UniProt
Find proteins for A0A9X9IKM4 (Bacteroides fragilis) Explore A0A9X9IKM4  Go to UniProtKB:  A0A9X9IKM4

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III-B CRISPR module RAMP protein Cmr4	C [auth D], D [auth E], E [auth F]	279	Bacteroides fragilis	Mutation(s): 1  Gene Names: cmr4, NXW39_14650
UniProt
Find proteins for A0A9X9NER2 (Bacteroides fragilis) Explore A0A9X9NER2  Go to UniProtKB:  A0A9X9NER2

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR type III-B/RAMP module-associated protein Cmr5	F [auth G], G [auth H]	136	Bacteroides fragilis	Mutation(s): 0  Gene Names: CQW34_02195, F2Z29_06595, F2Z89_11935, F3B44_04880, FSA06_24400, NXW39_14655, NXX45_16700
UniProt
Find proteins for A0A2M9V7H9 (Bacteroides fragilis) Explore A0A2M9V7H9  Go to UniProtKB:  A0A2M9V7H9

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RAMP superfamily protein	H [auth I]	314	Bacteroides fragilis	Mutation(s): 0  Gene Names: cmr6, CQW34_02194, F2Z89_11940, F3B44_04875, FSA06_24405, NXW39_14660, NXX45_16705
UniProt
Find proteins for A0A2M9V7I0 (Bacteroides fragilis) Explore A0A2M9V7I0  Go to UniProtKB:  A0A2M9V7I0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Type III-B CRISPR-associated protein Cas10/Cmr2	K [auth B]	600	Bacteroides fragilis	Mutation(s): 0  Gene Names: cas10, F2Z29_06610, F3B44_04895, FSA06_24385, NXW39_14640
UniProt
Find proteins for A0A5C6J4N7 (Bacteroides fragilis) Explore A0A5C6J4N7  Go to UniProtKB:  A0A5C6J4N7

Entity ID: 6
Molecule	Chains	Length	Organism	Image
CTR	I [auth K]	49	Bacteroides fragilis

Entity ID: 7
Molecule	Chains	Length	Organism	Image
RNA (49-MER)	J	49	Bacteroides fragilis

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	L [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
SAM (Subject of Investigation/LOI)	M [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
MN (Subject of Investigation/LOI)	N [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 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: 2025-11-26 
Deposition Author(s): Jin, X., Duan, B., Chen, Z., Zhao, B.

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

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release