[English] 日本語
Yorodumi
- EMDB-33185: CryoEM structure of type IV-A CasDinG bound NTS-nicked Csf-crRNA-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33185
TitleCryoEM structure of type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary complex in a second state
Map data
Sample
  • Complex: Type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary complex in a second state
    • Complex: Csf
      • Protein or peptide: Csf1
      • Protein or peptide: Csf3
      • Protein or peptide: Csf2
      • Protein or peptide: Csf5
      • Protein or peptide: Csf4
    • Complex: crRNA
      • RNA: crRNA
    • Complex: dsDNA
      • DNA: NTS
      • DNA: TS
  • Ligand: ZINC ION
KeywordsNuclease / STRUCTURAL PROTEIN-RNA-DNA COMPLEX
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsZhang JT / Cui N / Huang HD / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Cell / Year: 2023
Title: Type IV-A CRISPR-Csf complex: Assembly, dsDNA targeting, and CasDinG recruitment.
Authors: Ning Cui / Jun-Tao Zhang / Yongrui Liu / Yanhong Liu / Xiao-Yu Liu / Chongyuan Wang / Hongda Huang / Ning Jia /
Abstract: Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic ...Type IV CRISPR-Cas systems, which are primarily found on plasmids and exhibit a strong plasmid-targeting preference, are the only one of the six known CRISPR-Cas types for which the mechanistic details of their function remain unknown. Here, we provide high-resolution functional snapshots of type IV-A Csf complexes before and after target dsDNA binding, either in the absence or presence of CasDinG, revealing the mechanisms underlying Csf complex assembly, "DWN" PAM-dependent dsDNA targeting, R-loop formation, and CasDinG recruitment. Furthermore, we establish that CasDinG, a signature DinG family helicase, harbors ssDNA-stimulated ATPase activity and ATP-dependent 5'-3' DNA helicase activity. In addition, we show that CasDinG unwinds the non-target strand (NTS) and target strand (TS) of target dsDNA from the Csf complex. These molecular details advance our mechanistic understanding of type IV-A CRISPR-Csf function and should enable Csf complexes to be harnessed as genome-engineering tools for biotechnological applications.
History
DepositionApr 2, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33185.png

Downloads & links

-
Map

FileDownload / File: emd_33185.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. 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: 0.008
Minimum - Maximum-0.030970782 - 0.07178651
Average (Standard dev.)0.00008013353 (±0.001271464)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_33185_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33185_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33185_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary com...

EntireName: Type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary complex in a second state
Components
  • Complex: Type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary complex in a second state
    • Complex: Csf
      • Protein or peptide: Csf1
      • Protein or peptide: Csf3
      • Protein or peptide: Csf2
      • Protein or peptide: Csf5
      • Protein or peptide: Csf4
    • Complex: crRNA
      • RNA: crRNA
    • Complex: dsDNA
      • DNA: NTS
      • DNA: TS
  • Ligand: ZINC ION

+
Supramolecule #1: Type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary com...

SupramoleculeName: Type IV-A CasDinG bound NTS-nicked Csf-crRNA-dsDNA quaternary complex in a second state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

+
Supramolecule #2: Csf

SupramoleculeName: Csf / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #8
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

+
Supramolecule #3: crRNA

SupramoleculeName: crRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5

+
Supramolecule #4: dsDNA

SupramoleculeName: dsDNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6-#7

+
Macromolecule #1: Csf1

MacromoleculeName: Csf1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 28.675768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHHHHH MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLY GLSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR P EVVRKALS ...String:
HHHHHHHHHH MRYPSDIVDQ VLKAGPDKGL LTWEGVDAAC SHCSRPIQNG DLYSPSSVGA FFSDTRDLAS TSRSICWRCV VLRKKPMLY GLSAAVVTQD GIYSISKDVN KAWLFTTPPP APFLVVHSSS TMQHLSWRTP VTLDNRRIHV RYGPNLFIVR P EVVRKALS IADRVNEGQK KWVTPVYFDR KAAAMGHGLI TRAGAEMLTQ EEQEFFQSVT PGERWALSYL MHSKRPEPEV GE CITEKVM TSLNKE

+
Macromolecule #2: Csf3

MacromoleculeName: Csf3 / 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

+
Macromolecule #3: Csf2

MacromoleculeName: Csf2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 37.322234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQIEVTVRNI TPIFSAAPGS NYITIDGTIN PPPGVSRFPL VRTRMMYVAA DVGDGVIKSV PLQIVPGNTM RSLLRRTMLK HVIEPALVE KGNKLSIGAY ATAYSGNATG NPDGVPSSFD EIATMRAHPF IGLFGGGPRM LEGRLMVDSL YPIHTNAERI L GAGYENEM ...String:
MQIEVTVRNI TPIFSAAPGS NYITIDGTIN PPPGVSRFPL VRTRMMYVAA DVGDGVIKSV PLQIVPGNTM RSLLRRTMLK HVIEPALVE KGNKLSIGAY ATAYSGNATG NPDGVPSSFD EIATMRAHPF IGLFGGGPRM LEGRLMVDSL YPIHTNAERI L GAGYENEM MSGPITQVVW ARRMDPILNL GSSEDVEVIN GGAVAANGWI QDLLANSKAA ASKKKKAAAD EDESDGAAEE NG RGLKAFN AHEVVIPGLK WVWRISLDRP TDAQVGLVLL ALNKMTNERI AGGHSKDYGR FVIDGVSLNG EQVWSQSGIT GGE QYFDAV AEAIDGLSSK EFEQFAQSAK EA

+
Macromolecule #4: Csf5

MacromoleculeName: Csf5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 29.152414 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 LQLGQGGTRH AL SKWSHPQ FEKGGGSGGG SGGWSHPQFE K

+
Macromolecule #8: Csf4

MacromoleculeName: Csf4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 67.939883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MELPADALPG EGAVREVLRP LLKQAAEKTA AGKIVFAEAA TGTGKGRMIA SLAAAAAIKG DTVVVSAPLA VTWQLVNDMK DIPEVRRVG LTLSLGRPNF ISPQRTLEWA IDNERADLAA WIEGGGKPLS LRSMETSKVI SHELCWLLED ALLLAEDLPA D SLLLTSED ...String:
MELPADALPG EGAVREVLRP LLKQAAEKTA AGKIVFAEAA TGTGKGRMIA SLAAAAAIKG DTVVVSAPLA VTWQLVNDMK DIPEVRRVG LTLSLGRPNF ISPQRTLEWA IDNERADLAA WIEGGGKPLS LRSMETSKVI SHELCWLLED ALLLAEDLPA D SLLLTSED PADCPAQQLY VAMRSNYTEA GIILCSHFML AAHTRMMQMR GLGNDEELDD EAPTGLSLPH FIDTLIVDEA HL LEQAFAS VYTHTLRLRP LMRTIEGLGS RGRKPALDAL KELFTQMQVA SARSTNTSLN VPLSDVPELI PALKDTVKTL GAL PTKGMS RDARSVIRIA TRAANDALSG HSRLRIEVTP VHSYPMLLSG RSNLQRALLG LWNATGGATL VSATLFTTGD NGSL TRWKL EVPTERAAFL PPVHPAWTTA PVLLHKEFCA HEPDDSPEWA TECAQTIQGV ASTAQGGTLV LCTSYQNTEL LAGRL GAAL GDRLIVQSKT SSAATCLAQF KAKHKAGIRP VWLGLGAAWT GIDLSDHSLP DNPELDRLLS DLVITRIPVG QNRSLT HER RTAIGGFRII SQEAAWHFRQ GLGRLVRRPG VTHKNLWVLD ARIYGGAAWV APFRQILDRY KKA

+
Macromolecule #5: crRNA

MacromoleculeName: crRNA / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 19.89982 KDa
SequenceString:
GUGAACGGUG GAGCAACACC UGAAGGAAGG CUUGAUGAGC GUGUUCCCCG CAUACGCGGG (23G)

+
Macromolecule #6: NTS

MacromoleculeName: NTS / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 11.52044 KDa
SequenceString:
(DA)(DA)(DC)(DA)(DC)(DC)(DC)(DT)(DT)(DT) (DC)(DA)(DT)(DT)(DA)(DT)(DT)(DA)(DT)(DT) (DA)(DT)(DT)(DA)(DT)(DT)(DA)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)

+
Macromolecule #7: TS

MacromoleculeName: TS / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 16.547568 KDa
SequenceString: (DC)(DT)(DG)(DC)(DC)(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)(DG)(DA)(DA) ...String:
(DC)(DT)(DG)(DC)(DC)(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)(DG)(DA)(DA)(DA)(DG) (DG)(DG)(DT)(DG)(DT)(DT)

+
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

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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8882
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

+
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