[English] 日本語
Yorodumi
- EMDB-61479: Cryo-EM structure of RacrIC1-Cascade IC1-complex III -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-61479
TitleCryo-EM structure of RacrIC1-Cascade IC1-complex III
Map dataCryo-EM structure of RacrIC1-Cascade IC1-complex III
Sample
  • Complex: Cryo-EM structure of RacrIC1-Cascade IC1-complex III
    • Protein or peptide: CRISPR-associated protein, TM1801 family
    • Protein or peptide: CRISPR-associated protein, CT1133 family
    • RNA: RacrIC1 (124-MER)
Keywordscomplex / anti-CRISPR / Racr / cryo-EM / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
Function / homologyCRISPR-associated protein Csd2 / CRISPR-associated protein Cas7, subtype I-B/I-C / CRISPR-associated protein Cas7 / CRISPR-associated protein, Csd1-type / CRISPR-associated protein (Cas_Csd1) / maintenance of CRISPR repeat elements / CRISPR-associated protein, TM1801 family / CRISPR-associated protein, CT1133 family
Function and homology information
Biological speciesNitratidesulfovibrio vulgaris str. Hildenborough (bacteria) / Bifidobacterium pseudocatenulatum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWang H / Zhang S / Li S / Zhang K / Feng Y
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Structural insights into inhibition of CRISPR-Cas by RNA anti-CRISPRs
Authors: Wang H / Zhang S / Li S / Zhang K / Feng Y
History
DepositionSep 9, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_61479.png

Downloads & links

-
Map

FileDownload / File: emd_61479.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of RacrIC1-Cascade IC1-complex III
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.09100326 - 0.26038998
Average (Standard dev.)0.0006720691 (±0.008843417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Cryo-EM structure of RacrIC1-Cascade IC1-complex III

Fileemd_61479_additional_1.map
AnnotationCryo-EM structure of RacrIC1-Cascade IC1-complex III
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of RacrIC1-Cascade IC1-complex III

Fileemd_61479_half_map_1.map
AnnotationCryo-EM structure of RacrIC1-Cascade IC1-complex III
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Cryo-EM structure of RacrIC1-Cascade IC1-complex III

Fileemd_61479_half_map_2.map
AnnotationCryo-EM structure of RacrIC1-Cascade IC1-complex III
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of RacrIC1-Cascade IC1-complex III

EntireName: Cryo-EM structure of RacrIC1-Cascade IC1-complex III
Components
  • Complex: Cryo-EM structure of RacrIC1-Cascade IC1-complex III
    • Protein or peptide: CRISPR-associated protein, TM1801 family
    • Protein or peptide: CRISPR-associated protein, CT1133 family
    • RNA: RacrIC1 (124-MER)

-
Supramolecule #1: Cryo-EM structure of RacrIC1-Cascade IC1-complex III

SupramoleculeName: Cryo-EM structure of RacrIC1-Cascade IC1-complex III / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Molecular weightTheoretical: 470 KDa

-
Macromolecule #1: CRISPR-associated protein, TM1801 family

MacromoleculeName: CRISPR-associated protein, TM1801 family / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Molecular weightTheoretical: 32.227717 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: TAIANRYEFV LLFDVENGNP NGDPDAGNMP RIDPETGHGL VTDVCLKRKI RNHVALTKEG AERFNIYIQE KAILNETHER AYTACDLKP EPKKLPKKVE DAKRVTDWMC TNFYDIRTFG AVMTTEVNCG QVRGPVQMAF ARSVEPVVPQ EVSITRMAVT T KAEAEKQQ ...String:
TAIANRYEFV LLFDVENGNP NGDPDAGNMP RIDPETGHGL VTDVCLKRKI RNHVALTKEG AERFNIYIQE KAILNETHER AYTACDLKP EPKKLPKKVE DAKRVTDWMC TNFYDIRTFG AVMTTEVNCG QVRGPVQMAF ARSVEPVVPQ EVSITRMAVT T KAEAEKQQ GDNRTMGRKH IVPYGLYVAH GFISAPLAEK TGFSDEDLTL FWDALVNMFE HDRSAARGLM SSRKLIVFKH QN RLGNAPA HKLFDLVKVS RAEGSSGPAR SFADYAVTVG QAPEGVEVKE ML

UniProtKB: CRISPR-associated protein, TM1801 family

-
Macromolecule #2: CRISPR-associated protein, CT1133 family

MacromoleculeName: CRISPR-associated protein, CT1133 family / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Nitratidesulfovibrio vulgaris str. Hildenborough (bacteria)
Molecular weightTheoretical: 13.072887 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SLDPARTDRP YLLGRLFAVL EKAQEDAVPG ANATIKDRYL ASASANPGQV FHMLLKNASN HTAKLRKDPE RKGSAIHYEI MMQEIIDNI SDFPVTMSSD EQGLFMIGYY HQRKALF

UniProtKB: CRISPR-associated protein, CT1133 family

-
Macromolecule #3: RacrIC1 (124-MER)

MacromoleculeName: RacrIC1 (124-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Bifidobacterium pseudocatenulatum (bacteria)
Molecular weightTheoretical: 39.847746 KDa
SequenceString:
UGGAUCGAAA CACGACCUCG AGUCUGGUAA AGAAACCGCU GCUGCGAAAU UUGAACGCCA GCACAUGGAC UCGUCUACUA GCGCAGCUU AAUUAACCUA GGCUGCUGCC ACCGCUGAGC AAUAA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1677991
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 82089
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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