[English] 日本語
Yorodumi
- PDB-6nue: Small conformation of apo CRISPR_Csm complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6nue
TitleSmall conformation of apo CRISPR_Csm complex
Components
  • (CRISPR system ...) x 2
  • (CRISPR type III-associated RAMP protein ...) x 2
  • crRNA
KeywordsHYDROLASE / TRANSFERASE/RNA / CRISPR / Type III-A / ssRNAase / ssDNase / TRANSFERASE-RNA complex
Function / homologyCsm1 subunit domain B / HD domain / CRISPR Csm4 C-terminal domain / GGDEF domain profile. / RAMP superfamily / Csm2 Type III-A / HD domain / CRISPR-associated RAMP Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated protein, Csm2 Type III-A ...Csm1 subunit domain B / HD domain / CRISPR Csm4 C-terminal domain / GGDEF domain profile. / RAMP superfamily / Csm2 Type III-A / HD domain / CRISPR-associated RAMP Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / CRISPR-associated protein, Csm2 Type III-A / CRISPR type III-associated protein / CRISPR type III-associated RAMP protein Csm4 / GGDEF domain / 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
Specimen sourceStreptococcus thermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.3 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 Report
SummaryFull reportAbout validation report
DateDeposition: Jan 31, 2019 / Release: Mar 13, 2019

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-0519
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
J: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
A: CRISPR system Cms protein Csm2
B: CRISPR system Cms protein Csm2
C: CRISPR type III-associated RAMP protein Csm3
E: CRISPR type III-associated RAMP protein Csm3
H: crRNA
I: CRISPR type III-associated RAMP protein Csm4
M: CRISPR system Cms protein Csm2
N: CRISPR type III-associated RAMP protein Csm3
O: CRISPR type III-associated RAMP protein Csm3
P: CRISPR type III-associated RAMP protein Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,88012
Polyers309,37311
Non-polymers5071
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)45130
ΔGint (kcal/M)-238
Surface area (Å2)108490

-
Components

-
CRISPR system ... , 2 types, 4 molecules JABM

#1: Protein/peptide CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / ssDNase Cas10 / Cyclic oligoadenylate synthase / StCas10


Mass: 86930.672 Da / Num. of mol.: 1 / Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: cas10, csm1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A7HFE1, Hydrolases, Acting on ester bonds, Transferases, Transferring phosphorus-containing groups, Nucleotidyltransferases
#2: Protein/peptide CRISPR system Cms protein Csm2 / CRISPR type III A-associated protein Csm2


Mass: 14238.391 Da / Num. of mol.: 3 / Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A7HIX1

-
CRISPR type III-associated RAMP protein ... , 2 types, 6 molecules CENOPI

#3: Protein/peptide
CRISPR type III-associated RAMP protein Csm3 / Csm3 protein


Mass: 24600.918 Da / Num. of mol.: 5 / Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm3, CDA68_00842
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A7HIF0
#5: Protein/peptide CRISPR type III-associated RAMP protein Csm4 / Csm4 protein


Mass: 33786.949 Da / Num. of mol.: 1 / Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: csm4, CDA68_00841Sainte-Julienne Aerodrome
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A7HGA1

-
RNA chain / Non-polymers , 2 types, 2 molecules H

#4: RNA chain crRNA


Mass: 22935.553 Da / Num. of mol.: 1 / Source: (gene. exp.) Streptococcus thermophilus (bacteria)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Small conformation of apo CRISPR_Csm complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Streptococcus thermophilus (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.6
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

-
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
7UCSF Chimeramodel fitting
9PHENIX1.14model refinement
12cryoSPARC0.65classification
13cryoSPARC0.653D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 81540 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more