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- EMDB-8980: CasX ternary complex with 30bp target DNA -

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Basic information

Entry
Database: EMDB / ID: 8980
TitleCasX ternary complex with 30bp target DNA
Map dataCasX ternary complex with 30bp target
SampleCasX ternary complex with 30bp target DNA:
CasX / (nucleic-acidNucleic acid) x 3
Function / homologyUncharacterized protein
Function and homology information
SourceDeltaproteobacteria (bacteria) / Deltaproteobacteria bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsLiu JJ / Orlova N / Nogales E / Doudna JA
CitationJournal: Nature / Year: 2019
Title: CasX enzymes comprise a distinct family of RNA-guided genome editors.
Authors: Jun-Jie Liu / Natalia Orlova / Benjamin L Oakes / Enbo Ma / Hannah B Spinner / Katherine L M Baney / Jonathan Chuck / Dan Tan / Gavin J Knott / Lucas B Harrington / Basem Al-Shayeb / Alexander Wagner / Julian Brötzmann / Brett T Staahl / Kian L Taylor / John Desmarais / Eva Nogales / Jennifer A Doudna
Validation ReportPDB-ID: 6e5o

SummaryFull reportAbout validation report
DateDeposition: Jul 20, 2018 / Header (metadata) release: Jan 16, 2019 / Map release: Feb 6, 2019 / Last update: Feb 6, 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-6e5o
  • 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_8980.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
0.9 Å/pix.
= 230.4 Å
256 pix
0.9 Å/pix.
= 230.4 Å
256 pix
0.9 Å/pix.
= 230.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density
Contour Level:0.5 (by author), 0.5 (movie #1):
Minimum - Maximum-3.0629551 - 3.7386732
Average (Standard dev.)0.0035656285 (0.11046983)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin0.00.00.0
Limit255.0255.0255.0
Spacing256256256
CellA=B=C: 230.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.90.90.9
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z230.400230.400230.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-16-63-38
NX/NY/NZ727975
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-3.0633.7390.004

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Supplemental data

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Sample components

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Entire CasX ternary complex with 30bp target DNA

EntireName: CasX ternary complex with 30bp target DNA / Number of components: 5

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Component #1: protein, CasX ternary complex with 30bp target DNA

ProteinName: CasX ternary complex with 30bp target DNA / Recombinant expression: No
SourceSpecies: Deltaproteobacteria (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, CasX

ProteinName: CasX / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 113.096555 kDa
SourceSpecies: Deltaproteobacteria bacterium (bacteria)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: nucleic-acid, DNA (30-MER)

Nucleic-acidName: DNA (30-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DT)(DG)(DA)(DG)(DC)(DG)(DC)(DA) (DC)(DC)(DT)(DA)(DA)(DT)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DA)(DT)(DC)(DC)(DC)(DG)
MassTheoretical: 9.133892 kDa
SourceSpecies: Deltaproteobacteria bacterium (bacteria)

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Component #4: nucleic-acid, DNA (24-mer)

Nucleic-acidName: DNA (24-mer) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DG)(DG)(DG)(DA)(DT)(DT)(DT)(DC)(DA) (DT)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DC)(DA) (DG)(DA)(DA)(DA)
MassTheoretical: 7.378781 kDa
SourceSpecies: Deltaproteobacteria bacterium (bacteria)

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Component #5: nucleic-acid, RNA (122-MER)

Nucleic-acidName: RNA (122-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGCGCGUUUA UUCCAUUACU UUGGAGCCAG UCCCAGCGAC UAUGUCGUAU GGACGAAGCG CUUAUUUAUC GGAGAGAAAC CGAUAAGUAA AACGCAUCAA AGUGCUGCAG CAGAAAAUCA AA
MassTheoretical: 39.312418 kDa
SourceSpecies: Deltaproteobacteria bacterium (bacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
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: 46 e/Å2 / Illumination mode: SPOT SCAN
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: 258036
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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