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- EMDB-0516: Small conformation of ssRNA-bound CRISPR_Csm complex -

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Basic information

Entry
Database: EMDB / ID: 0516
TitleSmall conformation of ssRNA-bound CRISPR_Csm complex
Map dataSmall conformation of ssRNA-bound CRISPR_Csm complex
SampleSmall conformation of ssRNA-bound CRISPR_Csm complex
  • (CRISPR system ...) x 2
  • (nucleic-acidNucleic acid) x 2
  • (CRISPR type III-associated RAMP protein ...) x 2
  • ligand
Function / homologyHD domain / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / GGDEF domain profile. / RAMP superfamily / Csm2 Type III-A / HD domain / GGDEF domain / CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-associated protein / CRISPR-associated RAMP Csm3 ...HD domain / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / GGDEF domain profile. / RAMP superfamily / Csm2 Type III-A / HD domain / GGDEF domain / CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-associated protein / CRISPR-associated RAMP Csm3 / CRISPR-associated protein, Csm2 Type III-A / 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 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR type III-associated RAMP protein Csm4 / CRISPR type III-associated RAMP protein Csm3 / CRISPR system Cms protein Csm2
Function and homology information
SourceStreptococcus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsZhang K / Pintilie G / Li S / Zhu Y / Chiu W / Huang Z
CitationJournal: Cell Res. / Year: 2019
Title: Coupling of ssRNA cleavage with DNase activity in type III-A CRISPR-Csm revealed by cryo-EM and biochemistry.
Authors: Minghui Guo / Kaiming Zhang / Yuwei Zhu / Grigore D Pintilie / Xiaoyu Guan / Shanshan Li / Michael F Schmid / Zhuo Ma / Wah Chiu / Zhiwei Huang
Validation ReportPDB-ID: 6nud

SummaryFull reportAbout validation report
DateDeposition: Jan 31, 2019 / Header (metadata) release: Feb 27, 2019 / Map release: Mar 13, 2019 / Last update: Mar 13, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nud
  • Surface level: 0.5
  • 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_0516.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.06 Å/pix.
= 407.04 Å
384 pix
1.06 Å/pix.
= 407.04 Å
384 pix
1.06 Å/pix.
= 407.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-1.9540308 - 3.347922
Average (Standard dev.)0.00083021907 (0.0987355)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin0.00.00.0
Limit383.0383.0383.0
Spacing384384384
CellA=B=C: 407.03998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z407.040407.040407.040
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-1.9543.3480.001

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Supplemental data

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Sample components

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Entire Small conformation of ssRNA-bound CRISPR_Csm complex

EntireName: Small conformation of ssRNA-bound CRISPR_Csm complex / Number of components: 8

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Component #1: protein, Small conformation of ssRNA-bound CRISPR_Csm complex

ProteinName: Small conformation of ssRNA-bound CRISPR_Csm complex / Recombinant expression: No
SourceSpecies: Streptococcus thermophilus (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #2: protein, CRISPR system Cms protein Csm2

ProteinName: CRISPR system Cms protein Csm2 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 14.238391 kDa
SourceSpecies: Streptococcus thermophilus (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #3: nucleic-acid, crRNA

Nucleic-acidName: crRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
ACGGAAACUU UCGUAACUGU UUAAUUCUGU UCACUUAUUC CACCGAUAUA AACCUAAUUA CCUCGAGAGG GG
MassTheoretical: 22.935553 kDa
SourceSpecies: Streptococcus thermophilus (bacteria)

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Component #4: protein, CRISPR type III-associated RAMP protein Csm4

ProteinName: CRISPR type III-associated RAMP protein Csm4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.786949 kDa
SourceSpecies: Streptococcus thermophilus (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #5: protein, CRISPR system single-strand-specific deoxyribonuclease C...

ProteinName: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.930672 kDa
SourceSpecies: Streptococcus thermophilus (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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Component #6: nucleic-acid, target ssRNA

Nucleic-acidName: target ssRNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGGAAUAAGU GAACAGAAUU AAACAGUUAC GAAAAAAAAA AAGGGUACC
MassTheoretical: 15.980722 kDa
SourceSpecies: Streptococcus thermophilus (bacteria)

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Component #7: protein, CRISPR type III-associated RAMP protein Csm3

ProteinName: CRISPR type III-associated RAMP protein Csm3 / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 24.556908 kDa
SourceSpecies: Streptococcus thermophilus (bacteria)
Source (engineered)Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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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: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 7.6
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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: 7 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 / Number of projections: 50092
3D reconstructionSoftware: cryoSPARC / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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