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- PDB-9lq7: Cryo-EM structure of NTR-bound type III-B CRISPR-Cas effector complex -

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Basic information

Entry
Database: PDB / ID: 9lq7
TitleCryo-EM structure of NTR-bound type III-B CRISPR-Cas effector complex
Components
  • CRISPR type III-B/RAMP module-associated protein Cmr5
  • CRISPR-associated protein Cmr3
  • Cmr1
  • NTR
  • RAMP superfamily protein
  • Type III-B CRISPR module RAMP protein Cmr4
  • Type III-B CRISPR-associated protein Cas10/Cmr2
  • crRNA
KeywordsIMMUNE SYSTEM/RNA / CRISPR-Cas complex / adaptive immunity / RNA degradation / second messenger / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


defense response to virus / nucleotide binding / cytoplasm
Similarity search - Function
CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster ...CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / : / Cas10/Cmr2, second palm domain / CRISPR type III-associated protein / RAMP superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / S-ADENOSYLMETHIONINE / RNA / RNA (> 10) / CRISPR type III-B/RAMP module-associated protein Cmr5 / RAMP superfamily protein / Type III-B CRISPR-associated protein Cas10/Cmr2 / Uncharacterized protein / CRISPR-associated protein Cmr3 / Type III-B CRISPR module RAMP protein Cmr4
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsJin, X. / Duan, B. / Chen, Z. / Zhao, B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Chem Biol / Year: 2025
Title: Molecular basis of SAM-AMP synthesis and degradation in the type III-B CRISPR-Cas system.
Authors: Benzhen Duan / Xiaohui Jin / Xiaoman An / Yang Xiao / Qianxi Yang / Hongyu Zhao / Yunxiao Huang / Jingwen Wang / Qian Wang / Fenglei Du / Lu Lu / Lei Sun / Zhenguo Chen / Baoyu Zhao /
Abstract: Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers ...Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers immune responses. SAM-AMP can be degraded by NrN and SAM lyase, potentially deactivating the system. Here we find that the type III-B effector complex from Bacteroides fragilis uses a specific mechanism to recognize nonself target RNA and synthesize SAM-AMP. The 3' anti-tag of nonself target RNA induces conformational changes in the Cmr2 subunit, triggering SAM-AMP synthesis independently of the stalk loop of Cmr3 subunit. SAM-AMP binding induces NrN to transit from an open to a closed conformation, enabling hydrolysis of the 3'-5' phosphodiester bond. SAM lyase forms a triangular trimer that specifically degrades SAM-AMP into 5'-methylthioadenosine-AMP and homoserine lactone. These findings unveil unique mechanisms for SAM-AMP synthesis and degradation and provide deeper insights into the molecular basis of type III CRISPR-Cas signaling.
History
DepositionJan 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cmr1
B: Type III-B CRISPR-associated protein Cas10/Cmr2
C: CRISPR-associated protein Cmr3
D: Type III-B CRISPR module RAMP protein Cmr4
E: Type III-B CRISPR module RAMP protein Cmr4
F: Type III-B CRISPR module RAMP protein Cmr4
G: CRISPR type III-B/RAMP module-associated protein Cmr5
H: CRISPR type III-B/RAMP module-associated protein Cmr5
I: RAMP superfamily protein
K: NTR
J: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,06114
Polymers366,10011
Non-polymers9613
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 6 types, 9 molecules ABCDEFGHI

#1: Protein Cmr1


Mass: 55340.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: F2Z89_11915, F3B44_04900, NXW39_14635 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5M5QTL0
#2: Protein Type III-B CRISPR-associated protein Cas10/Cmr2


Mass: 69247.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: deletioins / Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: cas10, F2Z29_06610, F3B44_04895, FSA06_24385, NXW39_14640
Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C6J4N7
#3: Protein CRISPR-associated protein Cmr3


Mass: 49059.207 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: deletions / Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: NXW39_14645 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9X9IKM4
#4: Protein Type III-B CRISPR module RAMP protein Cmr4


Mass: 31537.041 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Gene: cmr4, NXW39_14650 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9X9NER2
#5: Protein CRISPR type III-B/RAMP module-associated protein Cmr5


Mass: 15273.493 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: CQW34_02195, F2Z29_06595, F2Z89_11935, F3B44_04880, FSA06_24400, NXW39_14655, NXX45_16700
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9V7H9
#6: Protein RAMP superfamily protein / Type III-B CRISPR module RAMP protein Cmr6


Mass: 35951.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria)
Gene: cmr6, CQW34_02194, F2Z89_11940, F3B44_04875, FSA06_24405, NXW39_14660, NXX45_16705
Production host: Escherichia coli (E. coli) / References: UniProt: A0A2M9V7I0

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RNA chain , 2 types, 2 molecules KJ

#7: RNA chain NTR


Mass: 15672.396 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: deletions / Source: (synth.) Bacteroides fragilis (bacteria)
#8: RNA chain crRNA


Mass: 15671.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: deletions / Source: (synth.) Bacteroides fragilis (bacteria)

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Non-polymers , 3 types, 3 molecules

#9: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#10: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NTR-bound type III-B CRISPR-Cas effector complex / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT
Source (natural)Organism: Bacteroides fragilis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67694 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00325439
ELECTRON MICROSCOPYf_angle_d0.61834733
ELECTRON MICROSCOPYf_dihedral_angle_d13.3544292
ELECTRON MICROSCOPYf_chiral_restr0.0513908
ELECTRON MICROSCOPYf_plane_restr0.0064154

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