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- PDB-9no4: Cryo-EM structure of Csm/AcrIIIA2/enolase 3:2 complex -

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Basic information

Entry
Database: PDB / ID: 9no4
TitleCryo-EM structure of Csm/AcrIIIA2/enolase 3:2 complex
Components
  • (CRISPR system Cms endoribonuclease ...) x 2
  • (CRISPR system Cms protein ...) x 3
  • AcrIIIA2
  • CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
  • Enolase
  • crRNA RNA (35-MER)
KeywordsRNA BINDING PROTEIN/RNA / ANTI-CRISPR / TYPE III CRISPR / CRYO-EM / STRUCTURAL BIOLOY / ANTI-BACTERIAL / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / exonuclease activity / peptidoglycan-based cell wall / glycolytic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus ...phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / exonuclease activity / peptidoglycan-based cell wall / glycolytic process / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / magnesium ion binding / cell surface / RNA binding / extracellular region / ATP binding
Similarity search - Function
: / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / Csm4, C-terminal / CRISPR Csm4 C-terminal domain / CRISPR-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / Csm2 Type III-A / : / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 ...: / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / Csm4, C-terminal / CRISPR Csm4 C-terminal domain / CRISPR-associated protein Csm5 / CRISPR-associated protein, Csm2 Type III-A / Csm2 Type III-A / : / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / Cas10/Cmr2, second palm domain / Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / : / CRISPR type III-associated protein / RAMP superfamily / HD domain / GGDEF domain profile. / GGDEF domain / HD domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR system Cms protein Csm5 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / Uncharacterized protein / CRISPR system Cms protein Csm4 / CRISPR system Cms protein Csm2 / CRISPR system Cms endoribonuclease Csm3 / Enolase
Similarity search - Component
Biological speciesStreptococcus thermophilus (bacteria)
Streptococcus phage 2972 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsGoswami, H.N. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM152081 United States
CitationJournal: To Be Published
Title: Cryo-EM structure of Csm/AcrIIIA2/enolase 3:2 complex
Authors: Goswami, H.N. / Li, H.
History
DepositionMar 7, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: CRISPR system Cms protein Csm4
E: CRISPR system Cms endoribonuclease Csm3
F: CRISPR system Cms endoribonuclease Csm3
G: CRISPR system Cms endoribonuclease Csm3
N: crRNA RNA (35-MER)
C: CRISPR system Cms protein Csm2
D: CRISPR system Cms protein Csm2
H: CRISPR system Cms protein Csm5
I: Enolase
J: Enolase
R: AcrIIIA2
K: Enolase
L: Enolase
M: Enolase
O: Enolase
P: Enolase
Q: Enolase
A: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)665,56526
Polymers665,37018
Non-polymers1948
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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CRISPR system Cms protein ... , 3 types, 4 molecules BCDH

#1: Protein CRISPR system Cms protein Csm4


Mass: 33828.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria)
Gene: csm, csm4, STCNRZ302_04685, STHERMO_1022, STHERMO_1028, STHERMO_1031
Production host: Escherichia coli (E. coli) / References: UniProt: A0A811IGE5
#5: Protein CRISPR system Cms protein Csm2 / CRISPR type III A-associated protein Csm2


Mass: 15361.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm, STHERMO_1026 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8D6U6W4
#6: Protein CRISPR system Cms protein Csm5 / CRISPR type III A-associated protein Csm5


Mass: 41226.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7HF79

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CRISPR system Cms endoribonuclease ... , 2 types, 3 molecules EFG

#2: Protein CRISPR system Cms endoribonuclease Csm3 / CRISPR type III A-associated RAMP protein Csm3


Mass: 24585.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm, STHERMO_1021 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAN1ZZJ5
#3: Protein CRISPR system Cms endoribonuclease Csm3 / CRISPR type III A-associated RAMP protein Csm3


Mass: 24555.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm, STHERMO_1021 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AAN1ZZJ5

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Protein , 3 types, 10 molecules IJKLMOPQRA

#7: Protein
Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 46948.484 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: eno, STER_0684 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03LI0, phosphopyruvate hydratase
#8: Protein AcrIIIA2


Mass: 12226.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage 2972 (virus) / Gene: CHPC1156_0026 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G8FB66
#9: Protein CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / ssDNase Cas10 / Cyclic oligoadenylate synthase / StCas10


Mass: 86930.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Cas10 / Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: cas10, csm1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A7HFE1, Hydrolases; Acting on ester bonds, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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RNA chain / Non-polymers , 2 types, 9 molecules N

#10: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: RNA chain crRNA RNA (35-MER)


Mass: 11118.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Production host: Escherichia coli (E. coli)

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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: Csm/AcrIIIA2/enolase complex / Type: COMPLEX
Details: AcrIIIA2 forms a stable ternary complex with the type III-A (Csm) crRNP (CRISPR RNA-Protein complex) and host enolase
Entity ID: #9, #1-#8 / Source: RECOMBINANT
Molecular weightValue: .680 MDa / Experimental value: NO
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5 / Details: 250mM NaCl, 30mM HEPES, 10mM Beta-mercaptoethanol
Buffer componentConc.: 250 mM / Name: Sodium Chloride / Formula: NaCl
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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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: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.21.2_5419model refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 311708 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.06 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.014847417
ELECTRON MICROSCOPYf_angle_d1.254164226
ELECTRON MICROSCOPYf_chiral_restr0.07377130
ELECTRON MICROSCOPYf_plane_restr0.01448289
ELECTRON MICROSCOPYf_dihedral_angle_d7.93496887

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