[English] 日本語
Yorodumi
- PDB-9nq7: Cryo-EM structure of Csm/AcrIIIA2/enolase 4:3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9nq7
TitleCryo-EM structure of Csm/AcrIIIA2/enolase 4:3 complex
Components
  • (CRISPR system ...) x 5
  • AcrIIIA2
  • Enolase
  • RNA (41-MER)
KeywordsRNA BINDING PROTEIN / ANTI-CRISPR / TYPE III CRISPR / CRYO-EM / STRUCTURAL BIOLOY / ANTI-BACTERIAL
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 vB_SthS-VA214 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 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 4:3 complex
Authors: Goswami, H.N. / Li, H.
History
DepositionMar 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
R: RNA (41-MER)
H: CRISPR system Cms protein Csm5
A: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
B: CRISPR system Cms protein Csm4
F: CRISPR system Cms endoribonuclease Csm3
D: CRISPR system Cms protein Csm2
C: CRISPR system Cms endoribonuclease Csm3
E: CRISPR system Cms endoribonuclease Csm3
G: CRISPR system Cms endoribonuclease Csm3
I: CRISPR system Cms protein Csm2
J: CRISPR system Cms protein Csm2
S: Enolase
L: Enolase
P: Enolase
K: Enolase
M: Enolase
O: Enolase
N: Enolase
Q: Enolase
T: AcrIIIA2


Theoretical massNumber of molelcules
Total (without water)709,77320
Polymers709,77320
Non-polymers00
Water00
1


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

-
Components

-
RNA chain , 1 types, 1 molecules R

#1: RNA chain RNA (41-MER)


Mass: 13055.781 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)

-
CRISPR system ... , 5 types, 10 molecules HABFCEGDIJ

#2: 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
#3: 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
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
#4: 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 endoribonuclease Csm3 / CRISPR type III A-associated RAMP protein Csm3


Mass: 24585.840 Da / Num. of mol.: 4
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
#6: Protein CRISPR system Cms protein Csm2 / CRISPR type III A-associated protein Csm2


Mass: 16190.501 Da / Num. of mol.: 3
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

-
Protein , 2 types, 9 molecules SLPKMONQT

#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: 12228.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus phage vB_SthS-VA214 (virus)
Gene: CHPC1156_0026 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G8FB66

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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: #2, #5, #7-#8, #3-#4, #6, #1 / 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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

-
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)

-
Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 325120 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 56.7 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.016450525
ELECTRON MICROSCOPYf_angle_d1.30868421
ELECTRON MICROSCOPYf_chiral_restr0.07277594
ELECTRON MICROSCOPYf_plane_restr0.01528812
ELECTRON MICROSCOPYf_dihedral_angle_d8.26327363

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more