[English] 日本語
Yorodumi
- PDB-8ip0: Cryo-EM structure of type I-B Cascade bound to a PAM-containing d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ip0
TitleCryo-EM structure of type I-B Cascade bound to a PAM-containing dsDNA target at 3.6 angstrom resolution
Components
  • (Type I-MYXAN CRISPR-associated protein ...) x 2
  • CRISPR associated protein Cas11b
  • DNA (41-MER)
  • DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
  • DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')
  • Fruiting body developmental protein R-like protein
  • RNA (44-MER)
KeywordsRNA BINDING PROTEIN/RNA/DNA / Type I-B / CRISPR-Cas / Cascade / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


defense response to virus
Similarity search - Function
CRISPR type MYXAN-associated protein Cmx8 / CRISPR-associated protein Cas5, N-terminal
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Uncharacterized protein / Fruiting body developmental protein R-like protein / Type I-MYXAN CRISPR-associated protein Cmx8
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6714 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXiao, Y. / Lu, M. / Yu, C. / Zhang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970547 China
Ministry of Science and Technology (MoST, China)2018YFA0902000 China
CitationJournal: To be published
Title: Cryo-EM structure of type I-B Cascade bound to a PAM-containing dsDNA target at 3.6 angstrom resolution.
Authors: Xiao, Y. / Lu, M. / Yu, C. / Zhang, Y.
History
DepositionMar 13, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
J: Type I-MYXAN CRISPR-associated protein Cmx8
A: Type I-MYXAN CRISPR-associated protein Cas5/Cmx5/DevS
B: Fruiting body developmental protein R-like protein
C: Fruiting body developmental protein R-like protein
D: Fruiting body developmental protein R-like protein
N: Fruiting body developmental protein R-like protein
O: Fruiting body developmental protein R-like protein
E: DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')
F: RNA (44-MER)
G: DNA (41-MER)
P: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
H: Fruiting body developmental protein R-like protein
I: Fruiting body developmental protein R-like protein
K: CRISPR associated protein Cas11b
L: CRISPR associated protein Cas11b
M: CRISPR associated protein Cas11b


Theoretical massNumber of molelcules
Total (without water)404,71716
Polymers404,71716
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Type I-MYXAN CRISPR-associated protein ... , 2 types, 2 molecules JA

#1: Protein Type I-MYXAN CRISPR-associated protein Cmx8 / CRISPR-associated protein Cas8b


Mass: 63703.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GenBank ID WP_071880939 / Source: (gene. exp.) Synechocystis sp. PCC 6714 (bacteria) / Gene: D082_50500
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A068N831
#2: Protein Type I-MYXAN CRISPR-associated protein Cas5/Cmx5/DevS / CRISPR-associated protein Cas5b / Type I-B CRISPR-associated protein Cas5


Mass: 26592.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6714 (bacteria) / Gene: D082_50520
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A068N1Y0

-
Protein , 2 types, 10 molecules BCDNOHIKLM

#3: Protein
Fruiting body developmental protein R-like protein / CRISPR-associated protein Cas7b / Type I-B CRISPR-associated protein Cas8


Mass: 33789.074 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6714 (bacteria) / Gene: D082_50510
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A068N458
#8: Protein CRISPR associated protein Cas11b


Mass: 14538.500 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6714 (bacteria) / Gene: D082_50500
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A068N831

-
DNA chain , 3 types, 3 molecules EGP

#4: DNA chain DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')


Mass: 4494.934 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PAM proximal non target DNA / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (41-MER)


Mass: 12725.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Target DNA / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3087.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: PAM distal non target DNA / Source: (synth.) synthetic construct (others)

-
RNA chain , 1 types, 1 molecules F

#5: RNA chain RNA (44-MER)


Mass: 13975.212 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: CRISPR RNA / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a PAM-containing dsDNA target presented as full R-loop formed state at 3.6 angstrom resolution
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Synechocystis sp. PCC 6714 (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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2100 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 92454 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00227355
ELECTRON MICROSCOPYf_angle_d0.64537513
ELECTRON MICROSCOPYf_dihedral_angle_d16.51710363
ELECTRON MICROSCOPYf_chiral_restr0.044078
ELECTRON MICROSCOPYf_plane_restr0.0044495

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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