[English] 日本語
Yorodumi
- PDB-8k21: Cas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8k21
TitleCas1-Cas2-dsDNA subregion in ICP1 Csy-DNA-Cas1-2/3 complex
Components
  • Cas1
  • DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')
  • HD Cas3-type domain-containing protein
KeywordsANTIBIOTIC/RNA BINDING PROTEIN/DNA / IMMUNE SYSTEM-RNA-DNA complex / ANTIBIOTIC-RNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / defense response to virus / hydrolase activity / DNA binding / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas1, YPEST subtype / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / CRISPR-associated nuclease/helicase Cas3, C-terminal / HD Cas3-type domain profile. / CRISPR-associated endonuclease Cas1, N-terminal domain / : / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / HD Cas3-type domain-containing protein / Cas1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsZhang, L.X. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: To Be Published
Title: Structure of csy complex with short DNA
Authors: Zhang, L.X. / Feng, Y.
History
DepositionJul 12, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
U: DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')
V: DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')
A: HD Cas3-type domain-containing protein
D: Cas1
E: Cas1
a: HD Cas3-type domain-containing protein
d: Cas1
e: Cas1


Theoretical massNumber of molelcules
Total (without water)163,5048
Polymers163,5048
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: DNA chain DNA (5'-D(P*AP*GP*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*GP*AP*T)-3')


Mass: 6543.286 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*AP*TP*CP*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*CP*T)-3')


Mass: 6338.120 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Production host: Escherichia coli (E. coli)
#3: Protein HD Cas3-type domain-containing protein


Mass: 8332.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00455 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5V9
#4: Protein
Cas1


Mass: 33489.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio phage ICP1_2004_A (virus) / Gene: TUST1-10_00460 / Production host: Escherichia coli (E. coli) / References: UniProt: F1D5W0

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: csy complex / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7
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: DARK FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30241 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00811754
ELECTRON MICROSCOPYf_angle_d1.26216051
ELECTRON MICROSCOPYf_dihedral_angle_d18.4041861
ELECTRON MICROSCOPYf_chiral_restr0.0711783
ELECTRON MICROSCOPYf_plane_restr0.0081884

+
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