[English] 日本語
Yorodumi
- EMDB-36828: Structure of Cas1-Cas2-dsDNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-36828
TitleStructure of Cas1-Cas2-dsDNA complex
Map data
Sample
  • Complex: csy complex
    • DNA: DNA (5'-D(P*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*G)-3')
    • DNA: DNA (5'-D(P*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*C)-3')
    • Protein or peptide: HD Cas3-type domain-containing protein
    • Protein or peptide: Cas1
KeywordsIMMUNE SYSTEM-RNA-DNA complex / ANTIBIOTIC
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / DNA endonuclease activity / helicase activity / defense response to virus / hydrolase activity / DNA binding / ATP 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, 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
HD Cas3-type domain-containing protein / Cas1
Similarity search - Component
Biological speciesVibrio phage ICP1_2004_A (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang LX / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: To Be Published
Title: Structure of Cas1-Cas2 complex bound dsDNA
Authors: Zhang LX / Feng Y
History
DepositionJul 12, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_36828.png

Downloads & links

-
Map

FileDownload / File: emd_36828.map.gz / Format: CCP4 / Size: 35.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 210 pix.
= 231. Å		1.1 Å/pix.
x 210 pix.
= 231. Å		1.1 Å/pix.
x 210 pix.
= 231. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.333
Minimum - Maximum-2.1036074 - 3.1149223
Average (Standard dev.)0.0040257224 (±0.07629867)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions210210210
Spacing210210210
CellA=B=C: 231.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_36828_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_36828_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : csy complex

EntireName: csy complex
Components
  • Complex: csy complex
    • DNA: DNA (5'-D(P*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*G)-3')
    • DNA: DNA (5'-D(P*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*C)-3')
    • Protein or peptide: HD Cas3-type domain-containing protein
    • Protein or peptide: Cas1

-
Supramolecule #1: csy complex

SupramoleculeName: csy complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)

-
Macromolecule #1: DNA (5'-D(P*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*G)-3')

MacromoleculeName: DNA (5'-D(P*CP*AP*AP*TP*TP*TP*AP*AP*AP*TP*AP*GP*GP*GP*AP*AP*G)-3')
type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 5.283474 KDa
SequenceString:
(DC)(DA)(DA)(DT)(DT)(DT)(DA)(DA)(DA)(DT) (DA)(DG)(DG)(DG)(DA)(DA)(DG)

-
Macromolecule #2: DNA (5'-D(P*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*C)-3')

MacromoleculeName: DNA (5'-D(P*TP*TP*CP*CP*CP*TP*AP*TP*TP*TP*AP*AP*AP*TP*TP*GP*C)-3')
type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 5.127345 KDa
SequenceString:
(DT)(DT)(DC)(DC)(DC)(DT)(DA)(DT)(DT)(DT) (DA)(DA)(DA)(DT)(DT)(DG)(DC)

-
Macromolecule #3: HD Cas3-type domain-containing protein

MacromoleculeName: HD Cas3-type domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 8.879253 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MFIRIKCFSK QPIAKKVSRE VSAYLEYTGN NTWEGHISGQ GVSNLQTKLI NVGKGVKVVC NYQDKVLFAI GNVAMSDTGS V

UniProtKB: HD Cas3-type domain-containing protein

-
Macromolecule #4: Cas1

MacromoleculeName: Cas1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Vibrio phage ICP1_2004_A (virus)
Molecular weightTheoretical: 33.60348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQKQILTSQK RNMYILSRCK VLVKNGQVCH LHEDGNVYTV PYANTVFIGL AEGTSITNEA MSMLAANGVI VFWTKGGGYD MFAADIICH LPQADYRPTK YMQNWVRLWL DEEKKLSAAK EILKMRVDSL STHVHDFGVD VENKRVSSIV NKFDKGVTQA T SFESLLGH ...String:
MQKQILTSQK RNMYILSRCK VLVKNGQVCH LHEDGNVYTV PYANTVFIGL AEGTSITNEA MSMLAANGVI VFWTKGGGYD MFAADIICH LPQADYRPTK YMQNWVRLWL DEEKKLSAAK EILKMRVDSL STHVHDFGVD VENKRVSSIV NKFDKGVTQA T SFESLLGH EGTFVKSLYK EYALEYEIEF KRDHKSADNY NKFLTLGNYY AYGIARSSLW ALGIDNSFPL LHGSTRRGGL VF DVADIIK TSIILPLAFH AADQGMSNTE FKRSCVAYFD KNDILAYLIN NIKRLCMEN

UniProtKB: Cas1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 99345
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

+
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