[English] 日本語
Yorodumi
- EMDB-31058: The Csy-AcrIF14 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31058
TitleThe Csy-AcrIF14 complex
Map data
Sample
  • Complex: The Csy-AcrIF14 complex
    • Complex: Csy
      • Protein or peptide: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4
      • Protein or peptide: Type I-F CRISPR-associated protein Csy1
      • Protein or peptide: CRISPR type I-F/YPEST-associated protein Csy2
      • Protein or peptide: CRISPR-associated protein Csy3
      • RNA: RNA (60-MER)
    • Complex: AcrIF14
      • Protein or peptide: AcrIF14
Keywordsinhibitor / complex / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


CRISPR-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)
Similarity search - Domain/homology
Tail protein / Uncharacterized protein / CRISPR-associated protein Csy3 / : / Uncharacterized protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Moraxella phage Mcat5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.43 Å
AuthorsZhang LX / Feng Y
CitationJournal: Nucleic Acids Res / Year: 2021
Title: Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR-Cas surveillance complex.
Authors: Xi Liu / Laixing Zhang / Yu Xiu / Teng Gao / Ling Huang / Yongchao Xie / Lingguang Yang / Wenhe Wang / Peiyi Wang / Yi Zhang / Maojun Yang / Yue Feng /
Abstract: CRISPR-Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of ...CRISPR-Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of both AcrIF14 and its complex with the crRNA-guided surveillance (Csy) complex. Our study demonstrates that apart from interacting with the Csy complex to block the hybridization of target DNA to the crRNA, AcrIF14 also endows the Csy complex with the ability to interact with non-sequence-specific dsDNA as AcrIF9 does. Further structural studies of the Csy-AcrIF14-dsDNA complex and biochemical studies uncover that the PAM recognition loop of the Cas8f subunit of the Csy complex and electropositive patches within the N-terminal domain of AcrIF14 are essential for the non-sequence-specific dsDNA binding to the Csy-AcrIF14 complex, which is different from the mechanism of AcrIF9. Our findings highlight the prevalence of Acr-induced non-specific DNA binding and shed light on future studies into the mechanisms of such Acr proteins.
History
DepositionMar 13, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ecv
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31058.png

Downloads & links

-
Map

FileDownload / File: emd_31058.map.gz / Format: CCP4 / Size: 30.5 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 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. 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: 0.028 / Movie #1: 0.035
Minimum - Maximum-0.24050418 - 0.38859177
Average (Standard dev.)0.0009039016 (±0.013051694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z220.000220.000220.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.2410.3890.001

-
Supplemental data

-
Sample components

-
Entire : The Csy-AcrIF14 complex

EntireName: The Csy-AcrIF14 complex
Components
  • Complex: The Csy-AcrIF14 complex
    • Complex: Csy
      • Protein or peptide: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4
      • Protein or peptide: Type I-F CRISPR-associated protein Csy1
      • Protein or peptide: CRISPR type I-F/YPEST-associated protein Csy2
      • Protein or peptide: CRISPR-associated protein Csy3
      • RNA: RNA (60-MER)
    • Complex: AcrIF14
      • Protein or peptide: AcrIF14

-
Supramolecule #1: The Csy-AcrIF14 complex

SupramoleculeName: The Csy-AcrIF14 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Csy

SupramoleculeName: Csy / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #6
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

-
Supramolecule #3: AcrIF14

SupramoleculeName: AcrIF14 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Moraxella phage Mcat5 (virus)

-
Macromolecule #1: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4

MacromoleculeName: Type I-F CRISPR-associated endoribonuclease Cas6/Csy4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 21.399451 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDHYLDIRLR PDPEFPPAQL MSVLFGKLHQ ALVAQGGDRI GVSFPDLDES RSRLGERLRI HASADDLRAL LARPWLEGLR DHLQFGEPA VVPHPTPYRQ VSRVQAKSNP ERLRRRLMRR HDLSEEEARK RIPDTVARAL DLPFVTLRSQ STGQHFRLFI R HGPLQATA EEGGFTCYGL SKGGFVPWF

UniProtKB: UNIPROTKB: A0A7G9X1S4

-
Macromolecule #2: Type I-F CRISPR-associated protein Csy1

MacromoleculeName: Type I-F CRISPR-associated protein Csy1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: CRISPR type I-F/YPEST-associated protein Csy2

MacromoleculeName: CRISPR type I-F/YPEST-associated protein Csy2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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 #4: CRISPR-associated protein Csy3

MacromoleculeName: CRISPR-associated protein Csy3 / type: protein_or_peptide / ID: 4 / Number of copies: 6 / 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 #5: AcrIF14

MacromoleculeName: AcrIF14 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Moraxella phage Mcat5 (virus)
Molecular weightTheoretical: 14.297373 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKKIEMIEIS QNRQNLTAFL HISEIKAINA KLADGVDVDK KSFDEICSIV LEQYQAKQIS NKQASEIFET LAKANKSFKI EKFRCSHGY NEIYKYSPDH EAYLFYCKGG QGQLNKLIAE NGRFM

UniProtKB: Tail protein

-
Macromolecule #6: RNA (60-MER)

MacromoleculeName: RNA (60-MER) / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.265404 KDa
SequenceString:
CUAAGAAAUU CACGGCGGGC UUGAUGUCCG CGUCUACCUG GUUCACUGCC GUGUAGGCAG

GENBANK: GENBANK: HQ326201.1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN
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

+
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126583
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