[English] 日本語
Yorodumi
- EMDB-61700: crRNA-guided surveillance (Csy) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61700
TitlecrRNA-guided surveillance (Csy) complex
Map data
Sample
  • Complex: Cys complex
    • Protein or peptide: Type I-F CRISPR-associated protein Csy1
    • Protein or peptide: Type I-F CRISPR-associated protein Csy2
    • Protein or peptide: Type I-F CRISPR-associated protein Csy3
    • RNA: RNA (60-MER)
Keywordscomplex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homologyCRISPR-associated protein Csy1 / CRISPR-associated protein (Cas_Csy1) / CRISPR-associated protein Csy2 / CRISPR-associated protein (Cas_Csy2) / CRISPR-associated protein Csy3 / CRISPR-associated protein (Cas_Csy3) / Type I-F CRISPR-associated protein Csy1 / Type I-F CRISPR-associated protein Csy2 / Type I-F CRISPR-associated protein Csy3
Function and homology information
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsWang WH / Guan LL / Du XY / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000901 China
CitationJournal: To Be Published
Title: crRNA-guided surveillance (Csy) complex
Authors: Wang WH / Guan LL / Du XY / Feng Y
History
DepositionSep 26, 2024-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61700.png

Downloads & links

-
Map

FileDownload / File: emd_61700.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 251.22 Å		0.84 Å/pix.
x 300 pix.
= 251.22 Å		0.84 Å/pix.
x 300 pix.
= 251.22 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8374 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.75989753 - 1.2855643
Average (Standard dev.)0.0007464266 (±0.04112825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.22 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_61700_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_61700_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_61700_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cys complex

EntireName: Cys complex
Components
  • Complex: Cys complex
    • Protein or peptide: Type I-F CRISPR-associated protein Csy1
    • Protein or peptide: Type I-F CRISPR-associated protein Csy2
    • Protein or peptide: Type I-F CRISPR-associated protein Csy3
    • RNA: RNA (60-MER)

-
Supramolecule #1: Cys complex

SupramoleculeName: Cys complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)

-
Macromolecule #1: Type I-F CRISPR-associated protein Csy1

MacromoleculeName: Type I-F CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 53.641059 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGSSHHHHHH SSGLVDYKDD DDKDYKDDDD KHGSHMASVS TGPNGEFSSP TLRQLIESFI QERLQGKLDK LKPDEDDKRQ ALLAGHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAPG QPGLAGSHEL ADELVSDVVG NAAALDVFKF L SLQYQGRY ...String:
MGSSHHHHHH SSGLVDYKDD DDKDYKDDDD KHGSHMASVS TGPNGEFSSP TLRQLIESFI QERLQGKLDK LKPDEDDKRQ ALLAGHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAPG QPGLAGSHEL ADELVSDVVG NAAALDVFKF L SLQYQGRY LLNWLTENSA EALQALSDDP EQAREWRQAF VGITAGKAAP ASHSLAKQLY FPLPGSGYHL LAPLFPTSLV QR VHGQIRE ARFGEAARAA REARQQKKPW PHGFSEYPNL AIQKFGGTKP QNISQLNSER HGENWLLASL PPHWEPQELR APL QQVSVF EHDLGRSPEV ARLTRTLRGF LATTKHNNLA IRQHRAQLVG QICDEALHYA ARLRELEPGW SASSDCRLHE AEQL WLDPL RVHTDEAFMR RRLWGDWPME VSERFANWLN RALTNKGLVM GEAESRQWRK DLGKELKMFK EILEDERD

UniProtKB: Type I-F CRISPR-associated protein Csy1

-
Macromolecule #2: Type I-F CRISPR-associated protein Csy2

MacromoleculeName: Type I-F CRISPR-associated protein Csy2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 36.093863 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF AHALQRRIGA TLDIELDGVG IICHRFEAQV SQPAGKHTLV FNLSRNPLN RDGSTAAIVE EGRAHLEVSL LLGVRGDGLD DHPAQEIARQ VQEQASAMRL AGGSILPRCN ERCPAPSAEL L MLGGSDEQ ...String:
MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF AHALQRRIGA TLDIELDGVG IICHRFEAQV SQPAGKHTLV FNLSRNPLN RDGSTAAIVE EGRAHLEVSL LLGVRGDGLD DHPAQEIARQ VQEQASAMRL AGGSILPRCN ERCPAPSAEL L MLGGSDEQ RRKNQRRLTR RLLPGFALVS REAMLQQHLE DLRSTTPEAT TLDALLDLSR LNFEPPATSP AEAASPLEAS WQ VRDKPGW LVPIPAGYNA LSPLYAPGEV RNARDRETPL RFVENLFSLG QWISPHRVTV LQDLLWYHQV EPDDGIYRWS TPR FAKHAI A

UniProtKB: Type I-F CRISPR-associated protein Csy2

-
Macromolecule #3: Type I-F CRISPR-associated protein Csy3

MacromoleculeName: Type I-F CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 37.534148 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSKQTLNTAS VLAFERKLDP SDALLSAGDW AQRDASQQWP AVSVIAKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNDQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG ...String:
MSKQTLNTAS VLAFERKLDP SDALLSAGDW AQRDASQQWP AVSVIAKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNDQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG EVARAWRFDA LAIGLRDFKA DAELDALAEL IASGLSGSGH VLLEVVAFAR IGDGQEVFPS QELILDKGDK KG QKSKTLY SVRDAAAIHS QKIGNALRTI DTWYPDEDGL GPIAVEPYGS VTSQGKAYRQ PKQKLDFYTL LDNWVLRDEA PAV EQQHYV IANLIRGGVF GEAEEK

UniProtKB: Type I-F CRISPR-associated protein Csy3

-
Macromolecule #4: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Molecular weightTheoretical: 19.377545 KDa
SequenceString:
CUAAGAAAUA GUGCAGCUUC UUAUGUAGAG AAAUGAACGA GUUCACUGCC GUGUAGGCAG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: OTHER / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131281
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