[English] 日本語
Yorodumi
- EMDB-48863: Type IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - l... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48863
TitleType IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - locked state
Map data
Sample
  • Complex: Type IV-A1 effector complex bound to CasDinG (locked state)
    • Protein or peptide: CRISPR type AFERR-associated protein Csf1 (Cas8)
    • Protein or peptide: CCRISPR type AFERR-associated protein Csf3 (Cas5)
    • Protein or peptide: CRISPR type AFERR-associated protein Csf2 (Cas7)
    • Protein or peptide: CRISPR type AFERR-associated protein Csf5 (Cas6)
    • RNA: crRNA (61-MER)
    • DNA: DNA, non-target strand (47-MER)
    • DNA: DNA, target strand (47-MER)
    • Protein or peptide: CRISPR-associated DEAD/DEAH-box helicase CasDinG
  • Ligand: ZINC ION
KeywordsCRISPR / transcriptional regulation / helicase / DNA BINDING PROTEIN
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / nucleobase-containing compound metabolic process / helicase activity / nucleic acid binding / ATP binding / metal ion binding
Similarity search - Function
: / CRISPR-associated protein Csf1 / CRISPR type IV associated protein Csf3 / : / Type IV CRISPR-associated endonuclease Csf5 / CRISPR-associated protein, Csf1 family / CRISPR type IV/AFERR-associated protein Csf2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CasDinG / Csf1 / Csf3 / Csf2 / Csf5
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsKiernan KA / Taylor DW
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM138348 United States
Welch FoundationF-1938-20200401 United States
American Cancer SocietyRSG-21-050-01-DMC United States
CitationJournal: To Be Published
Title: Locked and loaded: mechanisms of CasDinG recruitment to the type IV-A1 CRISPR effector complex
Authors: Kiernan KA / Taylor DW
History
DepositionFeb 1, 2025-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48863.png

Downloads & links

-
Map

FileDownload / File: emd_48863.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å		0.83 Å/pix.
x 512 pix.
= 426.598 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8332 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.32744005 - 1.2788124
Average (Standard dev.)0.004425407 (±0.032989614)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.5984 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : Type IV-A1 effector complex bound to CasDinG (locked state)

EntireName: Type IV-A1 effector complex bound to CasDinG (locked state)
Components
  • Complex: Type IV-A1 effector complex bound to CasDinG (locked state)
    • Protein or peptide: CRISPR type AFERR-associated protein Csf1 (Cas8)
    • Protein or peptide: CCRISPR type AFERR-associated protein Csf3 (Cas5)
    • Protein or peptide: CRISPR type AFERR-associated protein Csf2 (Cas7)
    • Protein or peptide: CRISPR type AFERR-associated protein Csf5 (Cas6)
    • RNA: crRNA (61-MER)
    • DNA: DNA, non-target strand (47-MER)
    • DNA: DNA, target strand (47-MER)
    • Protein or peptide: CRISPR-associated DEAD/DEAH-box helicase CasDinG
  • Ligand: ZINC ION

+
Supramolecule #1: Type IV-A1 effector complex bound to CasDinG (locked state)

SupramoleculeName: Type IV-A1 effector complex bound to CasDinG (locked state)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

+
Macromolecule #1: CRISPR type AFERR-associated protein Csf1 (Cas8)

MacromoleculeName: CRISPR type AFERR-associated protein Csf1 (Cas8) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 27.036002 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLYG LSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR PEVVRKALSI A DRVNEGQK ...String:
MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLYG LSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR PEVVRKALSI A DRVNEGQK KWVTPVYFDR KAAAMGHGLI TRAGAEMLTQ EEQEFFQSVT PGERWALSYL MHSKRPEPEV GECITEKVMT SL N

UniProtKB: Csf1

+
Macromolecule #2: CCRISPR type AFERR-associated protein Csf3 (Cas5)

MacromoleculeName: CCRISPR type AFERR-associated protein Csf3 (Cas5) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 24.421953 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVNLKVTIDL SNPMMEPGDL LHLDALLGAL RVSRARAEHG DAINPRDYHY DLPLERYQAP SGDWVFKASA FKLKRQLPNQ MWMQTGRLS IVEAARHRQS GYLQLRAGKP NPAGGPFKTS IYHRPIVQAE LTAFCVGDQQ GIEALLSECR QIGGKRGVGF G QVAGFKVE ...String:
MVNLKVTIDL SNPMMEPGDL LHLDALLGAL RVSRARAEHG DAINPRDYHY DLPLERYQAP SGDWVFKASA FKLKRQLPNQ MWMQTGRLS IVEAARHRQS GYLQLRAGKP NPAGGPFKTS IYHRPIVQAE LTAFCVGDQQ GIEALLSECR QIGGKRGVGF G QVAGFKVE PVAETDCPWS WRALPADADP RLVTSEHARC IAAIRGPYWD RTLHVEALAP TP

UniProtKB: Csf3

+
Macromolecule #3: CRISPR type AFERR-associated protein Csf2 (Cas7)

MacromoleculeName: CRISPR type AFERR-associated protein Csf2 (Cas7) / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 38.623707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MWSHPQFEKG AMQIEVTVRN ITPIFSAAPG SNYITIDGTI NPPPGVSRFP LVRTRMMYVA ADVGDGVIKS VPLQIVPGNT MRSLLRRTM LKHVIEPALV EKGNKLSIGA YATAYSGNAT GNPDGVPSSF DEIATMRAHP FIGLFGGGPR MLEGRLMVDS L YPIHTNAE ...String:
MWSHPQFEKG AMQIEVTVRN ITPIFSAAPG SNYITIDGTI NPPPGVSRFP LVRTRMMYVA ADVGDGVIKS VPLQIVPGNT MRSLLRRTM LKHVIEPALV EKGNKLSIGA YATAYSGNAT GNPDGVPSSF DEIATMRAHP FIGLFGGGPR MLEGRLMVDS L YPIHTNAE RILGAGYENE MMSGPITQVV WARRMDPILN LGSSEDVEVI NGGAVAANGW IQDLLANSKA AASKKKKAAA DE DESDGAA EENGRGLKAF NAHEVVIPGL KWVWRISLDR PTDAQVGLVL LALNKMTNER IAGGHSKDYG RFVIDGVSLN GEQ VWSQSG ITGGEQYFDA VAEAIDGLSS KEFEQFAQSA KEA

UniProtKB: Csf2

+
Macromolecule #4: CRISPR type AFERR-associated protein Csf5 (Cas6)

MacromoleculeName: CRISPR type AFERR-associated protein Csf5 (Cas6) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 25.398381 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFVKQVFFDL GARIHADEAR ALVAKLLDDT QPGLVSALMN YMPASKTSKT EFPLVQFSNF NQGFALLGFG EVGAQILSDA TPIIHDAMA KLFASRGQGV VVQVSSRDVP LSCEKRPYGL QYTVAKMVVQ KKHEHRERLA NPETGKVFLE GLFLRSLERQ A AAVGMVLP ...String:
MFVKQVFFDL GARIHADEAR ALVAKLLDDT QPGLVSALMN YMPASKTSKT EFPLVQFSNF NQGFALLGFG EVGAQILSDA TPIIHDAMA KLFASRGQGV VVQVSSRDVP LSCEKRPYGL QYTVAKMVVQ KKHEHRERLA NPETGKVFLE GLFLRSLERQ A AAVGMVLP RDLVVSFKGA ERVSSVKLRP DSTLAHGSLR HAVFEVNARL GGLWSVGFLL SKGFGHINTD LQLG

UniProtKB: Csf5

+
Macromolecule #8: CRISPR-associated DEAD/DEAH-box helicase CasDinG

MacromoleculeName: CRISPR-associated DEAD/DEAH-box helicase CasDinG / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 81.111812 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASWSHPQFE KGAENLYFQS NAMKLAQGAF VDVIRIGALS PPTDQRSLWA RTLLSEAVDQ GLDSLPVPLQ DVSTFTVTLQ PALAVRLKA LADQHNTPVS VYAAGLIEAM RRRSESGSVA EAPMELPADA LPGEGAVREV LRPLLKQAAE KTAAGKIVFA E AATGTGKG ...String:
MASWSHPQFE KGAENLYFQS NAMKLAQGAF VDVIRIGALS PPTDQRSLWA RTLLSEAVDQ GLDSLPVPLQ DVSTFTVTLQ PALAVRLKA LADQHNTPVS VYAAGLIEAM RRRSESGSVA EAPMELPADA LPGEGAVREV LRPLLKQAAE KTAAGKIVFA E AATGTGKG RMIASLAAAA AIKGDTVVVS APLAVTWQLV NDMKDIPEVR RVGLTLSLGR PNFISPQRTL EWAIDNERAD LA AWIEGGG KPLSLRSMET SKVISHELCW LLEDALLLAE DLPADSLLLT SEDPADCPAQ QLYVAMRSNY TEAGIILCSH FML AAHTRM MQMRGLGNDE ELDDEAPTGL SLPHFIDTLI VDEAHLLEQA FASVYTHTLR LRPLMRTIEG LGSRGRKPAL DALK ELFTQ MQVASARSTN TSLNVPLSDV PELIPALKDT VKTLGALPTK GMSRDARSVI RIATRAANDA LSGHSRLRIE VTPVH SYPM LLSGRSNLQR ALLGLWNATG GATLVSATLF TTGDNGSLTR WKLEVPTERA AFLPPVHPAW TTAPVLLHKE FCAHEP DDS PEWATECAQT IQGVASTAQG GTLVLCTSYQ NTELLAGRLG AALGDRLIVQ SKTSSAATCL AQFKAKHKAG IRPVWLG LG AAWTGIDLSD HSLPDNPELD RLLSDLVITR IPVGQNRSLT HERRTAIGGF RIISQEAAWH FRQGLGRLVR RPGVTHKN L WVLDARIYGG AAWVAPFRQI LDRYKKA

UniProtKB: CasDinG

+
Macromolecule #5: crRNA (61-MER)

MacromoleculeName: crRNA (61-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.837855 KDa
SequenceString:
GUGAACGGUG GAGCAACACC UGAAGGAAGG CUUGAUGAGC GUGUUCCCCG CAUACGCGGG G

+
Macromolecule #6: DNA, non-target strand (47-MER)

MacromoleculeName: DNA, non-target strand (47-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.603382 KDa
SequenceString:
(DT)(DC)(DA)(DC)(DG)(DC)(DT)(DA)(DG)(DT) (DG)(DG)(DA)(DG)(DC)(DA)(DA)(DC)(DA)(DC) (DC)(DT)(DG)(DA)(DA)(DG)(DG)(DA)(DA) (DG)(DG)(DC)(DT)(DT)(DG)(DA)(DT)(DG)(DA) (DG) (DC)(DA)(DA)(DG)(DT)(DG)(DC)

+
Macromolecule #7: DNA, target strand (47-MER)

MacromoleculeName: DNA, target strand (47-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.349179 KDa
SequenceString:
(DG)(DC)(DA)(DC)(DT)(DT)(DG)(DC)(DT)(DC) (DA)(DT)(DC)(DA)(DA)(DG)(DC)(DC)(DT)(DT) (DC)(DC)(DT)(DT)(DC)(DA)(DG)(DG)(DT) (DG)(DT)(DT)(DG)(DC)(DT)(DC)(DC)(DA)(DC) (DT) (DA)(DG)(DC)(DG)(DT)(DG)(DA)

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38045
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelPDB ID:

7xg3


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9n3z:
Type IV-A1 CRISPR effector complex bound to dsDNA and CasDinG - locked state

+
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