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- EMDB-9708: Cryo-EM structure of Csm effector complex -

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Basic information

Entry
Database: EMDB / ID: 9708
TitleCryo-EM structure of Csm effector complex
Map data
SampleToCsm effector complex:
Csm1 / Csm2 / Csm3 / Csm4Sainte-Julienne Aerodrome / Csm5 / nucleic-acidNucleic acid / ligand
Function / homologyHD domain / HD domain profile. / HD/PDEase domain / CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-associated protein / HD domain / CRISPR-associated protein, Csm2 Type III-A / CRISPR-associated protein Csm5 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated RAMP Csm3 ...HD domain / HD domain profile. / HD/PDEase domain / CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-associated protein / HD domain / CRISPR-associated protein, Csm2 Type III-A / CRISPR-associated protein Csm5 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated RAMP Csm3 / GGDEF domain / Csm2 Type III-A / RAMP superfamily / GGDEF domain profile. / identical protein binding / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
SourceThermococcus onnurineus NA1 (archaea) / Thermococcus onnurineus (strain NA1) (archaea)
Methodsingle particle reconstruction / cryo EM / 3.35 Å resolution
AuthorsHuo Y / Li T / Wang N / Dong Q / Wang X / Jiang T
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 ReportPDB-ID: 6iqw

SummaryFull reportAbout validation report
DateDeposition: Nov 9, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Jan 16, 2019 / Last update: Jan 16, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6iqw
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9708.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
240 pix
1.04 Å/pix.
= 249.6 Å
240 pix
1.04 Å/pix.
= 249.6 Å
240 pix
1.04 Å/pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour Level:3.27 (by author), 4 (movie #1):
Minimum - Maximum-13.652025999999999 - 21.464327000000001
Average (Standard dev.)-0.007533303 (1.2889774)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S213
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-13.65221.464-0.008

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Supplemental data

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Sample components

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Entire ToCsm effector complex

EntireName: ToCsm effector complex / Number of components: 8

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Component #1: protein, ToCsm effector complex

ProteinName: ToCsm effector complex / Recombinant expression: No
SourceSpecies: Thermococcus onnurineus NA1 (archaea)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Csm1

ProteinName: Csm1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 88.131898 kDa
SourceSpecies: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Csm2

ProteinName: Csm2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.410691 kDa
SourceSpecies: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Csm3

ProteinName: Csm3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 32.721936 kDa
SourceSpecies: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Csm4

ProteinName: Csm4Sainte-Julienne Aerodrome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.345061 kDa
SourceSpecies: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Csm5

ProteinName: Csm5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.262145 kDa
SourceSpecies: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: nucleic-acid, RNA (5'-R(*GP*UP*GP*GP*AP*AP*AP*GP*UP*GP*GP*CP*CP*C...

Nucleic-acidName: 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')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GUGGAAAGUG GCCCGAAACC CUUC
MassTheoretical: 7.707653 kDa
SourceSpecies: Thermococcus onnurineus (strain NA1) (archaea) / Strain: NA1

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Component #8: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: 3D array / Method: cryo EM
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.875 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 61924
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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