[English] 日本語
Yorodumi
- EMDB-31186: Structure of Csy-AcrIF24-dsDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31186
TitleStructure of Csy-AcrIF24-dsDNA
Map data
Sample
  • Complex: Csy-AcrIF24-dsDNA
    • Complex: Csy-AcrIF24
      • Protein or peptide: CRISPR type I-F/YPEST-associated protein Csy2
      • Protein or peptide: CRISPR-associated protein Csy3
      • Protein or peptide: type I-F CRISPR-associated endoribonuclease Cas6/Csy4
      • Protein or peptide: AcrIF24
      • RNA: RNA (60-MER)
      • Protein or peptide: Type I-F CRISPR-associated protein Csy1
    • Complex: dsDNA
      • DNA: 54-MER DNA
      • DNA: 54-MER DNA
Keywordscomplex / inhibitor / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA-DNA 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) / Uncharacterized protein / CRISPR-associated protein Csy3 / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang L / Feng Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31822012 China
CitationJournal: Nat Commun / Year: 2022
Title: Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24.
Authors: Lingguang Yang / Laixing Zhang / Peipei Yin / Hao Ding / Yu Xiao / Jianwei Zeng / Wenhe Wang / Huan Zhou / Qisheng Wang / Yi Zhang / Zeliang Chen / Maojun Yang / Yue Feng /
Abstract: CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the ...CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding.
History
DepositionApr 12, 2021-
Header (metadata) releaseApr 20, 2022-
Map releaseApr 20, 2022-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31186.png

Downloads & links

-
Map

FileDownload / File: emd_31186.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 343.744 Å		1.07 Å/pix.
x 320 pix.
= 343.744 Å		1.07 Å/pix.
x 320 pix.
= 343.744 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.036224063 - 0.10409247
Average (Standard dev.)0.00024988415 (±0.0024426626)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 343.74402 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Csy-AcrIF24-dsDNA

EntireName: Csy-AcrIF24-dsDNA
Components
  • Complex: Csy-AcrIF24-dsDNA
    • Complex: Csy-AcrIF24
      • Protein or peptide: CRISPR type I-F/YPEST-associated protein Csy2
      • Protein or peptide: CRISPR-associated protein Csy3
      • Protein or peptide: type I-F CRISPR-associated endoribonuclease Cas6/Csy4
      • Protein or peptide: AcrIF24
      • RNA: RNA (60-MER)
      • Protein or peptide: Type I-F CRISPR-associated protein Csy1
    • Complex: dsDNA
      • DNA: 54-MER DNA
      • DNA: 54-MER DNA

+
Supramolecule #1: Csy-AcrIF24-dsDNA

SupramoleculeName: Csy-AcrIF24-dsDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

+
Supramolecule #2: Csy-AcrIF24

SupramoleculeName: Csy-AcrIF24 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6

+
Supramolecule #3: dsDNA

SupramoleculeName: dsDNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8

+
Macromolecule #1: CRISPR type I-F/YPEST-associated protein Csy2

MacromoleculeName: CRISPR type I-F/YPEST-associated protein Csy2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 36.244074 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF VHALQRRVGI SLDIELDGVG IVCHRFEAQI SQPAGKRTKV FNLTRNPLN RDGSTAAIVE EGRAHLEVSL LLGVHGDGLD DHPAQEIARQ VQEQAGAMRL AGGSILPWCN ERFPAPNAEL L MLGGSDEQ ...String:
MSVTDPEALL LLPRLSIQNA NAISSPLTWG FPSPGAFTGF VHALQRRVGI SLDIELDGVG IVCHRFEAQI SQPAGKRTKV FNLTRNPLN RDGSTAAIVE EGRAHLEVSL LLGVHGDGLD DHPAQEIARQ VQEQAGAMRL AGGSILPWCN ERFPAPNAEL L MLGGSDEQ RRKNQRRLTR RLLPGFALVS REALLQQHLE TLRTTLPEAT TLDALLDLCR INFEPPATSS EEEASPPDAA WQ VRDKPGW LVPIPAGYNA LSPLYLPGEV RNARDRETPL RFVENLFGLG EWLSPHRVAA LSDLLWYHHA EPDKGLYRWS TPR FVEHAI A

UniProtKB: Uncharacterized protein

+
Macromolecule #2: CRISPR-associated protein Csy3

MacromoleculeName: CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 37.623324 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSKPILSTAS VLAFERKLDP SDALMSAGAW AQRDASQEWP AVTVREKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNEQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG ...String:
MSKPILSTAS VLAFERKLDP SDALMSAGAW AQRDASQEWP AVTVREKSVR GTISNRLKTK DRDPAKLDAS IQSPNLQTVD VANLPSDAD TLKVRFTLRV LGGAGTPSAC NDAAYRDKLL QTVATYVNEQ GFAELARRYA HNLANARFLW RNRVGAEAVE V RINHIRQG EVARTWRFDA LAIGLRDFKA DAELDALAEL IASGLSGSGH VLLEVVAFAR IGDGQEVFPS QELILDKGDK KG QKSKTLY SVRDAAAIHS QKIGNALRTI DTWYPDEDGL GPIAVEPYGS VTSQGKAYRQ PKQKLDFYTL LDNWVLRDEA PAV EQQHYV IANLIRGGVF GEAEEK

UniProtKB: CRISPR-associated protein Csy3

+
Macromolecule #3: type I-F CRISPR-associated endoribonuclease Cas6/Csy4

MacromoleculeName: type I-F CRISPR-associated endoribonuclease Cas6/Csy4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 21.429477 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDHYLDIRLR PDPEFPPAQL MSVLFGKLHQ ALVAQGGDRI GVSFPDLDES RSRLGERLRI HASADDLRAL LARPWLEGLR DHLQFGEPA VVPHPTPYRQ VSRVQAKSNP ERLRRRLMRR HDLSEEEARK RIPDTVARTL DLPFVTLRSQ STGQHFRLFI R HGPLQATA EEGGFTCYGL SKGGFVPWF

+
Macromolecule #4: AcrIF24

MacromoleculeName: AcrIF24 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 24.995271 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNAIHIGPFS ITPAARGLHY GGLPHHQWTL YYGPREMAIK TLPDSYTSSE VRDEFSDIIA EFVIDARHRY APDVLELVNS DGDAVLARV AVSRLPEALS GCIPDDRFPY WLLTASRPRL GLPVTLNEYT ALAVELSAPP LAWITGLLPG EVLTHDAEEW R PPTSWELR ...String:
MNAIHIGPFS ITPAARGLHY GGLPHHQWTL YYGPREMAIK TLPDSYTSSE VRDEFSDIIA EFVIDARHRY APDVLELVNS DGDAVLARV AVSRLPEALS GCIPDDRFPY WLLTASRPRL GLPVTLNEYT ALAVELSAPP LAWITGLLPG EVLTHDAEEW R PPTSWELR HVVGEGSFTG VSGAAAAALL GMSATNFRKY TAGDSAANRQ KISFAAWHYL LDRLGVKRAS

+
Macromolecule #6: Type I-F CRISPR-associated protein Csy1

MacromoleculeName: Type I-F CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 49.313254 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTSPLPTPTW QELRQFIESF IQERLQGKLD KLHPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EAVQALSDNA EQAREWRQAF I GITAVKGA ...String:
MTSPLPTPTW QELRQFIESF IQERLQGKLD KLHPDEDDKR QTLLATHRRE AWLADAARRV GQLQLVTHTL KPIHPDARGS NLHSLPQAP GQPGLAGSHE LGDRLVSDVV GNAAALDVFK FLSLQYQGKN LLNWLTEDSA EAVQALSDNA EQAREWRQAF I GITAVKGA PASHSLAKQL YFPLPGSGYH LLAPLFPTSL VHHVHALLRE ARFGDAAKAA REARSRQESW PHGFSEYPNL AI QKFGGTK PQNISQLNSE RYGENWLLPS LPPHWQRQDQ RAPIRHSSVF EHDFGRSPEV SRLTRTLQRL LAKTRHNNFT IRR YRAQLV GQICDEALQY AARLRELEPG WSATPGCQLH DAEQLWLDPL RAQTDETFLQ RRLRGDWPAE VGNRFANWLN RAVS SDSQI LGSPEAAQWS QELSKELTMF KEILEDERD

UniProtKB: Uncharacterized protein

+
Macromolecule #5: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 5 / Number of copies: 2
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.265404 KDa
SequenceString:
CUAAGAAAUU CACGGCGGGC UUGAUGUCCG CGUCUACCUG GUUCACUGCC GUGUAGGCAG

GENBANK: GENBANK: HQ326201.1

+
Macromolecule #7: 54-MER DNA

MacromoleculeName: 54-MER DNA / type: dna / ID: 7 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 16.708691 KDa
SequenceString: (DG)(DG)(DA)(DA)(DG)(DC)(DC)(DA)(DT)(DC) (DC)(DA)(DG)(DG)(DT)(DA)(DG)(DA)(DC)(DG) (DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC)(DA) (DA)(DG)(DC)(DC)(DC)(DG)(DC)(DC)(DG)(DT) (DG) (DA)(DA)(DG)(DG)(DT)(DG) ...String:
(DG)(DG)(DA)(DA)(DG)(DC)(DC)(DA)(DT)(DC) (DC)(DA)(DG)(DG)(DT)(DA)(DG)(DA)(DC)(DG) (DC)(DG)(DG)(DA)(DC)(DA)(DT)(DC)(DA) (DA)(DG)(DC)(DC)(DC)(DG)(DC)(DC)(DG)(DT) (DG) (DA)(DA)(DG)(DG)(DT)(DG)(DC)(DA) (DG)(DC)(DT)(DG)(DC)(DT)

+
Macromolecule #8: 54-MER DNA

MacromoleculeName: 54-MER DNA / type: dna / ID: 8 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 16.574561 KDa
SequenceString: (DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DC)(DA) (DC)(DC)(DT)(DT)(DC)(DA)(DC)(DG)(DG)(DC) (DG)(DG)(DG)(DC)(DT)(DT)(DG)(DA)(DT) (DG)(DT)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DT) (DA) (DC)(DC)(DT)(DG)(DG)(DA) ...String:
(DA)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DC)(DA) (DC)(DC)(DT)(DT)(DC)(DA)(DC)(DG)(DG)(DC) (DG)(DG)(DG)(DC)(DT)(DT)(DG)(DA)(DT) (DG)(DT)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DT) (DA) (DC)(DC)(DT)(DG)(DG)(DA)(DT)(DG) (DG)(DC)(DT)(DT)(DC)(DC)

-
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: OTHER / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1564735
CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 364290
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