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- PDB-6e5o: CasX ternary complex with 30bp target DNA -

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Database: PDB / ID: 6e5o
TitleCasX ternary complex with 30bp target DNA
  • CasX
  • DNA (24-mer)
  • DNA (30-MER)
  • RNA (122-MER)
Function / homologyUncharacterized protein
Function and homology information
Specimen sourceDeltaproteobacteria bacterium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsLiu, J.J. / Orlova, N. / Nogales, E. / Doudna, J.A.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jul 20, 2018 / Release: Feb 6, 2019

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Deposited unit
Y: CasX
C: DNA (30-MER)
D: DNA (24-mer)
B: RNA (122-MER)

Theoretical massNumber of molelcules
Total (without water)168,9224

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Protein/peptide CasX

Mass: 113096.555 Da / Num. of mol.: 1
Source: (gene. exp.) Deltaproteobacteria bacterium (bacteria)
Gene: DD725_10130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A357BT59
#2: DNA chain DNA (30-MER)

Mass: 9133.892 Da / Num. of mol.: 1 / Source: (synth.) Deltaproteobacteria bacterium (bacteria)
#3: DNA chain DNA (24-mer)

Mass: 7378.781 Da / Num. of mol.: 1 / Source: (synth.) Deltaproteobacteria bacterium (bacteria)
#4: RNA chain RNA (122-MER)

Mass: 39312.418 Da / Num. of mol.: 1 / Source: (synth.) Deltaproteobacteria bacterium (bacteria)

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

Sample preparation

ComponentName: CasX ternary complex with 30bp target DNA / Type: COMPLEX / Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Source (natural)Organism: Deltaproteobacteria (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)


SoftwareName: PHENIX / Version: 1.14_3260 / Classification: refinement
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 258036 / Symmetry type: POINT

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