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- EMDB-6777: Electron cryo-microscopy structure of LbuCas13a-crRNA binary complex -

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Basic information

Entry
Database: EMDB / ID: 6777
TitleElectron cryo-microscopy structure of LbuCas13a-crRNA binary complex
SampleLbuCas13a-crRNA binary complex
SourceLeptotrichia buccalis / bacteria / レプトトリキア・ブカリス
Map dataElectron cryo-microscopy structure of LbuCas13a-crRNA binary complex
Methodsingle particle reconstruction, at 3.2 Å resolution
AuthorsZhang X / Wang Y
CitationCell, 2017, 170, 714-726.e10

Cell, 2017, 170, 714-726.e10 StrPapers
The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a.
Liang Liu / Xueyan Li / Jun Ma / Zongqiang Li / Lilan You / Jiuyu Wang / Min Wang / Xinzheng Zhang / Yanli Wang

Validation ReportPDB-ID: 5xwy

SummaryFull reportAbout validation report
DateDeposition: Jun 30, 2017 / Header (metadata) release: Sep 13, 2017 / Map release: Sep 13, 2017 / Last update: Sep 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5xwy
  • Surface level: 0.02
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_6777.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
0.82 Å/pix.
= 164. Å
200 pix
0.82 Å/pix.
= 164. Å
200 pix
0.82 Å/pix.
= 164. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 0.82 Å
Density
Contour Level:0.02 (by author), 0.02 (movie #1):
Minimum - Maximum-0.12865293 - 0.20330638
Average (Standard dev.)0.00039493514 (0.0066677476)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions200200200
Origin000
Limit199199199
Spacing200200200
CellA=B=C: 164 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z164.000164.000164.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.1290.2030.000

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Supplemental data

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Sample components

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Entire LbuCas13a-crRNA binary complex

EntireName: LbuCas13a-crRNA binary complex / Number of components: 3

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Component #1: protein, LbuCas13a-crRNA binary complex

ProteinName: LbuCas13a-crRNA binary complex / Recombinant expression: No
SourceSpecies: Leptotrichia buccalis / bacteria / レプトトリキア・ブカリス
Strain: ATCC 14201
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a

ProteinName: A type VI-A CRISPR-Cas RNA-guided RNA ribonuclease, Cas13a
Recombinant expression: No
MassTheoretical: 138.555156 kDa
Source (engineered)Expression System: Leptotrichia buccalis (strain atcc 14201 / dsm 1135 / jcm 12969 / nctc 10249 / c-1013-b) / bacteria
Strain: ATCC 14201 / DSM 1135 / JCM 12969 / NCTC 10249 / C-1013-b

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Component #3: nucleic-acid, RNA (59-MER)

Nucleic-acidName: RNA (59-MER) / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GGACCACCCC AAAAAUGAAG GGGACUAAAA CACAAAUCUA UCUGAAUAAA CUCUUCUUC
MassTheoretical: 18.869348 kDa

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Experimental details

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Sample preparation

Specimen stateparticle
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: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 238758
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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