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- PDB-6iqw: Cryo-EM structure of Csm effector complex -

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Basic information

Entry
Database: PDB / ID: 6iqw
TitleCryo-EM structure of Csm effector complex
Components
  • Csm1
  • Csm2
  • Csm3
  • Csm4
  • Csm5Saint-Michel-des-Saints Aerodrome
  • RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
KeywordsRNA BINDING PROTEIN/RNA / Cryo-EM structure / CRISPR / Csm / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


exonuclease activity / defense response to virus / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / ATP binding / identical protein binding
RAMP superfamily / CRISPR type III-associated protein / Csm2 Type III-A / Csm1 subunit domain B / HD domain / Csm1, subunit domain B / CRISPR-associated RAMP Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated protein Csm5 / HD domain ...RAMP superfamily / CRISPR type III-associated protein / Csm2 Type III-A / Csm1 subunit domain B / HD domain / Csm1, subunit domain B / CRISPR-associated RAMP Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated protein Csm5 / HD domain / CRISPR-associated protein, Csm2 Type III-A / CRISPR type III-associated RAMP protein Csm4 / HD/PDEase domain / GGDEF domain
Uncharacterized protein / Uncharacterized protein / CRISPR system Cms protein Csm4 / Uncharacterized protein / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
Biological speciesThermococcus onnurineus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsHuo, Y. / Li, T. / Wang, N. / Dong, Q. / Wang, X. / Jiang, T.
Funding support China, 2items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08010301 China
National Science Foundation (China)31670750 China
CitationJournal: Cell Res. / Year: 2018
Title: Cryo-EM structure of Type III-A CRISPR effector complex.
Authors: Yangao Huo / Tao Li / Nan Wang / Qinghua Dong / Xiangxi Wang / Tao Jiang /
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
A: Csm1
B: Csm2
C: Csm3
D: Csm3
E: Csm4
F: Csm5
I: RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,8098
Polymers261,3017
Non-polymers5071
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26750 Å2
ΔGint-126 kcal/mol
Surface area83520 Å2

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Components

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Protein , 5 types, 6 molecules ABCDEF

#1: Protein Csm1 /


Mass: 88131.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0893 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWB8
#2: Protein Csm2


Mass: 22410.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0894 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWB9
#3: Protein Csm3


Mass: 32721.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0895 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC0
#4: Protein Csm4


Mass: 32345.061 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0896 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC1
#5: Protein Csm5 / Saint-Michel-des-Saints Aerodrome


Mass: 45262.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Gene: TON_0897 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC2

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RNA chain / Non-polymers , 2 types, 2 molecules I

#6: RNA chain RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*CP*GP*AP*AP*AP*CP*CP*CP*UP*UP*C)-3')


Mass: 7707.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (strain NA1) (archaea)
Strain: NA1 / Production host: Escherichia coli (E. coli)
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: ToCsm effector complex / Type: COMPLEX / Entity ID: 1,2,3,4,5,6 / Source: RECOMBINANT
Source (natural)Organism: Thermococcus onnurineus NA1 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 1.875 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3247: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61924 / Symmetry type: POINT

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