[English] 日本語
![](img/lk-miru.gif)
- PDB-7uzx: Staphylococcus epidermidis RP62a CRISPR effector subcomplex with ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7uzx | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Staphylococcus epidermidis RP62a CRISPR effector subcomplex with non-self target RNA bound | |||||||||||||||
![]() |
| |||||||||||||||
![]() | HYDROLASE/RNA / Type IIIA CRISPR / effector complex / ![]() | |||||||||||||||
Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Smith, E.M. / Ferrell, S.H. / Tokars, V.L. / Mondragon, A. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Structures of an active type III-A CRISPR effector complex. Authors: Eric M Smith / Sé Ferrell / Valerie L Tokars / Alfonso Mondragón / ![]() Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) provide many prokaryotes with an adaptive immune system against invading genetic material. ...Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) provide many prokaryotes with an adaptive immune system against invading genetic material. Type III CRISPR systems are unique in that they can degrade both RNA and DNA. In response to invading nucleic acids, they produce cyclic oligoadenylates that act as secondary messengers, activating cellular nucleases that aid in the immune response. Here, we present seven single-particle cryo-EM structures of the type III-A Staphylococcus epidermidis CRISPR effector complex. The structures reveal the intact S. epidermidis effector complex in an apo, ATP-bound, cognate target RNA-bound, and non-cognate target RNA-bound states and illustrate how the effector complex binds and presents crRNA. The complexes bound to target RNA capture the type III-A effector complex in a post-RNA cleavage state. The ATP-bound structures give details about how ATP binds to Cas10 to facilitate cyclic oligoadenylate production. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 334.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 273.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 26921MC ![]() 7uzwC ![]() 7uzyC ![]() 7uzzC ![]() 7v00C ![]() 7v01C ![]() 7v02C M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
Components
#1: Protein | Mass: 24033.975 Da / Num. of mol.: 5 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 35984 / RP62A / References: UniProt: Q5HK91 #2: Protein | | Mass: 34551.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 35984 / RP62A / References: UniProt: Q5HK92 #3: Protein | | Mass: 87685.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 35984 / RP62A / References: UniProt: Q5HK89 #4: RNA chain | | Mass: 11811.033 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: ATCC 35984 / RP62A #5: RNA chain | | Mass: 12789.641 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
-
Sample preparation
Component | Name: Staphylococcus epidermidis RP62a CRISPR effector subcomplex with target RNA bound Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||
Specimen | Conc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||
Specimen support | Details: cryo-EM grids were prepared by glow discharging for 10 seconds at 15 mA in a Pelco easiGlow glow discharger. Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-1.2/1.3 | ||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K Details: 3 ul of the protein-RNA complex were added to the grid and allowed to incubate for 10 seconds. After incubation the grid was blotted in a Vitrobot Mark IV (FEI Thermo Fischer) (humidity 95% ...Details: 3 ul of the protein-RNA complex were added to the grid and allowed to incubate for 10 seconds. After incubation the grid was blotted in a Vitrobot Mark IV (FEI Thermo Fischer) (humidity 95% and temperature 4 C) for 3 seconds with a force of 0 before plunge freezing in liquid ethane. |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 49.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 2455 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||||||||||
CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2368249 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 168418 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: THROUGHOUT | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 178.69 Å2 / Biso mean: 71.7477 Å2 / Biso min: 20 Å2 |