[English] 日本語
Yorodumi
- EMDB-9535: Cryo-EM Structure of the PaeCas3-AcrF3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9535
TitleCryo-EM Structure of the PaeCas3-AcrF3 complex
Map dataCryo-EM structure of PaeCas3-AcrF3 complex
Sample
  • Complex: PaeCas3-AcrF3 complex
    • Complex: type I-F CRISPR-associated nuclease/helicase Cas3
      • Protein or peptide: type I-F CRISPR-associated nuclease/helicase Cas3
    • Complex: anti-CRISPR protein 3 (AcrF3)
      • Protein or peptide: anti-CRISPR protein 3 (AcrF3)
Function / homology
Function and homology information


helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / defense response to virus / Hydrolases; Acting on ester bonds / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / Cas3, HD domain ...: / Cas3 inhibitor AcrF3 / Helicase Cas3, CRISPR-associated, Yersinia-type / : / : / CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain / CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain / CRISPR-associated Cas3-type HD domain / CRISPR-associated Cas3-type HD domain superfamily / Cas3, HD domain / HD Cas3-type domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Phage protein / CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / Pseudomonas phage JBD5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsZhang X / Ma J / Wang Y / Wang J
CitationJournal: Cell Res / Year: 2016
Title: A CRISPR evolutionary arms race: structural insights into viral anti-CRISPR/Cas responses.
Authors: Jiuyu Wang / Jun Ma / Zhi Cheng / Xu Meng / Lilan You / Min Wang / Xinzheng Zhang / Yanli Wang /
History
DepositionAug 7, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseSep 21, 2016-
UpdateOct 19, 2016-
Current statusOct 19, 2016Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5gqh
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9535.png

Downloads & links

-
Map

FileDownload / File: emd_9535.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of PaeCas3-AcrF3 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 140 pix.
= 114.8 Å		0.82 Å/pix.
x 140 pix.
= 114.8 Å		0.82 Å/pix.
x 140 pix.
= 114.8 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: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.1324326 - 0.19505402
Average (Standard dev.)0.0014116985 (±0.019745765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 114.799995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.820.820.82
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z114.800114.800114.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-0.1320.1950.001

-
Supplemental data

-
Sample components

-
Entire : PaeCas3-AcrF3 complex

EntireName: PaeCas3-AcrF3 complex
Components
  • Complex: PaeCas3-AcrF3 complex
    • Complex: type I-F CRISPR-associated nuclease/helicase Cas3
      • Protein or peptide: type I-F CRISPR-associated nuclease/helicase Cas3
    • Complex: anti-CRISPR protein 3 (AcrF3)
      • Protein or peptide: anti-CRISPR protein 3 (AcrF3)

-
Supramolecule #1: PaeCas3-AcrF3 complex

SupramoleculeName: PaeCas3-AcrF3 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 158 kDa/nm

-
Supramolecule #2: type I-F CRISPR-associated nuclease/helicase Cas3

SupramoleculeName: type I-F CRISPR-associated nuclease/helicase Cas3 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria) / Recombinant plasmid: pET

-
Supramolecule #3: anti-CRISPR protein 3 (AcrF3)

SupramoleculeName: anti-CRISPR protein 3 (AcrF3) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Pseudomonas phage JBD5 (virus)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria) / Recombinant plasmid: pET

-
Macromolecule #1: type I-F CRISPR-associated nuclease/helicase Cas3

MacromoleculeName: type I-F CRISPR-associated nuclease/helicase Cas3 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SQDPMNILLV SQCEKRALSE TRRILDQFAE RRGERTWQTP ITQAGLDTLR RLLKKSARRN TAVACHWIRG RDHSELLWIV GDASRFNAQG AVPTNRTCRD ILRKEDENDW HSAEDIRLLT VMAALFHDIG KASQAFQAKL RNRGKPMADA YRHEWVSLRL ...String:
MGSSHHHHHH SQDPMNILLV SQCEKRALSE TRRILDQFAE RRGERTWQTP ITQAGLDTLR RLLKKSARRN TAVACHWIRG RDHSELLWIV GDASRFNAQG AVPTNRTCRD ILRKEDENDW HSAEDIRLLT VMAALFHDIG KASQAFQAKL RNRGKPMADA YRHEWVSLRL FEAFVGPGSS DEDWLRRLAD KRETGDAWLS QLARDDRQSA PPGPFQKSRL PPLAQAVGWL IVSHHRLPNG DHRGSASLAR LPAPIQSQWC GARDADAKEK AACWQFPHGL PFASAHWRAR TALCAQSMLE RPGLLARGPA LLHDSYVMHV SRLILMLADH HYSSLPADSR LGDPNFPLHA NTDRDSGKLK QRLDEHLLGV ALHSRKLAGT LPRLERQLPR LARHKGFTRR VEQPRFRWQD KAYDCAMACR EQAMEHGFFG LNLASTGCGK TLANGRILYA LADPQRGARF SIALGLRSLT LQTGQAYRER LGLGDDDLAI LVGGSAAREL FEKQQERLER SGSESAQELL AENSHVHFAG TLEDGPLREW LGRNSAGNRL LQAPILACTI DHLMPASESL RGGHQIAPLL RLMTSDLVLD EVDDFDIDDL PALSRLVHWA GLFGSRVLLS SATLPPALVQ GLFEAYRSGR EIFQRHRGAP GRATEIRCAW FDEFSSQSSA HGAVTSFSEA HATFVAQRLA KLEQLPPRRQ AQLCTVHAAG EARPALCREL AGQMNTWMAD LHRCHHTEHQ GRRISFGLLR LANIEPLIEL AQAILAQGAP EGLHVHLCVY HSRHPLLVRS AIERQLDELL KRSDDDAAAL FARPTLAKAL QASTERDHLF VVLASPVAEV GRDHDYDWAI VEPSSMRSII QLAGRIRRHR SGFSGEANLY LLSRNIRSLE GQNPAFQRPG FETPDFPLDS HDLHDLLDPA LLARIDASPR IVEPFPLFPR SRLVDLEHRR LRALMLADDP PSSLLGVPLW WQTPASLSGA LQTSQPFRAG AKERCYALLP DEDDEERLHF SRYEEGTWSN QDNLLRNLDL TYGPRIQTWG TVNYREELVA MAGREDLDLR QCAMRYGEVR LRENTQGWSY HPYLGFKKYN

-
Macromolecule #2: anti-CRISPR protein 3 (AcrF3)

MacromoleculeName: anti-CRISPR protein 3 (AcrF3) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas phage JBD5 (virus)
Recombinant expressionOrganism: Escherichia Coli BL21(DE3) (bacteria)
SequenceString:
MSNTISDRIV ARSVIEAARF IQSWEDADPD SLTEDQVLAA AGFAARLHEG LQATVLQRLV DESNHEEYRE FKAWEEALLN ADGRVASSPF ADWGWWYRIA NVMLATASQN VGVTWGSRVH GRLMAIFQDK FKQRYEEQA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
GridModel: GiG-322 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 16 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 8.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND3
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4q2c

Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 78480

-
Atomic model buiding 1

RefinementProtocol: BACKBONE TRACE
Output model

PDB-5gqh:
Cryo-EM structure of PaeCas3-AcrF3 complex

+
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