[English] 日本語
Yorodumi
- EMDB-35629: Cryo-EM structure of type I-B Cascade bound to a PAM-containing d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35629
TitleCryo-EM structure of type I-B Cascade bound to a PAM-containing dsDNA target at 3.6 angstrom resolution
Map data
Sample
  • Complex: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a PAM-containing dsDNA target presented as full R-loop formed state at 3.6 angstrom resolution
    • Protein or peptide: Type I-MYXAN CRISPR-associated protein Cmx8
    • Protein or peptide: Type I-MYXAN CRISPR-associated protein Cas5/Cmx5/DevS
    • Protein or peptide: Fruiting body developmental protein R-like protein
    • DNA: DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')
    • RNA: RNA (44-MER)
    • DNA: DNA (41-MER)
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
    • Protein or peptide: CRISPR associated protein Cas11b
KeywordsType I-B / CRISPR-Cas / Cascade / RNA BINDING PROTEIN/RNA/DNA / RNA BINDING PROTEIN-RNA-DNA complex
Function / homologyCRISPR type MYXAN-associated protein Cmx8 / CRISPR-associated protein Cas5, N-terminal / defense response to virus / Uncharacterized protein / Fruiting body developmental protein R-like protein / Type I-MYXAN CRISPR-associated protein Cmx8
Function and homology information
Biological speciesSynechocystis sp. PCC 6714 (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsXiao Y / Lu M / Yu C / Zhang Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970547 China
Ministry of Science and Technology (MoST, China)2018YFA0902000 China
CitationJournal: To be published
Title: Cryo-EM structure of type I-B Cascade bound to a PAM-containing dsDNA target at 3.6 angstrom resolution.
Authors: Xiao Y / Lu M / Yu C / Zhang Y
History
DepositionMar 13, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35629.png

Downloads & links

-
Map

FileDownload / File: emd_35629.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-0.36412668 - 1.5517225
Average (Standard dev.)0.0017086442 (±0.04988404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 396.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35629_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35629_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a...

EntireName: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a PAM-containing dsDNA target presented as full R-loop formed state at 3.6 angstrom resolution
Components
  • Complex: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a PAM-containing dsDNA target presented as full R-loop formed state at 3.6 angstrom resolution
    • Protein or peptide: Type I-MYXAN CRISPR-associated protein Cmx8
    • Protein or peptide: Type I-MYXAN CRISPR-associated protein Cas5/Cmx5/DevS
    • Protein or peptide: Fruiting body developmental protein R-like protein
    • DNA: DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')
    • RNA: RNA (44-MER)
    • DNA: DNA (41-MER)
    • DNA: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
    • Protein or peptide: CRISPR associated protein Cas11b

-
Supramolecule #1: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a...

SupramoleculeName: Cryo-EM structure of Synechocystis sp. PCC6714 Cascade bound to a PAM-containing dsDNA target presented as full R-loop formed state at 3.6 angstrom resolution
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)

-
Macromolecule #1: Type I-MYXAN CRISPR-associated protein Cmx8

MacromoleculeName: Type I-MYXAN CRISPR-associated protein Cmx8 / type: protein_or_peptide / ID: 1 / Details: GenBank ID WP_071880939 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Molecular weightTheoretical: 63.703344 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MPKTQAEILT LDFNLAELPS AQHRAGLAGL ILMIRELKKW PWFKIRQKEK DVLLSIENLD QYGASIQLNL EGLIALFDLA YLSFTEERK SKSKIKDFKR VDEIEIEENG KNKIQKYYFY DVITPQGGFL AGWDKSDGQI WLRIWRDMFW SIIKGVPATR N PFNNRCGL ...String:
MPKTQAEILT LDFNLAELPS AQHRAGLAGL ILMIRELKKW PWFKIRQKEK DVLLSIENLD QYGASIQLNL EGLIALFDLA YLSFTEERK SKSKIKDFKR VDEIEIEENG KNKIQKYYFY DVITPQGGFL AGWDKSDGQI WLRIWRDMFW SIIKGVPATR N PFNNRCGL NLNAGDSFSK DVESVWKSLQ NAEKTTGQSG AFYLGAMAVN AENVSTDDLI KWQFLLHFWA FVAQVYCPYI LD KDGKRNF NGYVIVIPDI ANLEDFCDIL PDVLSNRNSK AFGFRPQESV IDVPEQGALE LLNLIKQRIA KKAGSGLLSD LIV GVEVIH AEKQGNSIKL HSVSYLQPNE ESVDDYNAIK NSYYCPWFRR QLLLNLVNPK FDLASQSWLK RHPWYGFGDL LSRI PQRWL KENNSYFSHD ARQLFTQKGD FDMTVATTKT REYAEIVYKI AQGFVLSKLS SKHDLQWSKC KGNPKLEREY NDKKE KVVN EAFLAIRSRT EKQAFIDYFV STLYPHVRQD EFVDFAQKLF QDTDEIRSLT LLALSSQYPI KRQGETE

UniProtKB: Type I-MYXAN CRISPR-associated protein Cmx8

-
Macromolecule #2: Type I-MYXAN CRISPR-associated protein Cas5/Cmx5/DevS

MacromoleculeName: Type I-MYXAN CRISPR-associated protein Cas5/Cmx5/DevS / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Molecular weightTheoretical: 26.592424 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAQLALALDT VTRYLRLKAP FAAFRPFQSG SFRSTTPVPS FSAVYGLLLN LAGIEQRQEV EGKVTLIKPK AELPKLAIAI GQVKPSSTS LINQQLHNYP VGNSGKEFAS RTFGSKYWIA PVRREVLVNL DLIIGLQSPV EFWQKLDQGL KGETVINRYG L PFAGDNNF ...String:
MAQLALALDT VTRYLRLKAP FAAFRPFQSG SFRSTTPVPS FSAVYGLLLN LAGIEQRQEV EGKVTLIKPK AELPKLAIAI GQVKPSSTS LINQQLHNYP VGNSGKEFAS RTFGSKYWIA PVRREVLVNL DLIIGLQSPV EFWQKLDQGL KGETVINRYG L PFAGDNNF LFDEIYPIEK PDLASWYCPL EPDTRPNQGA CRLTLWIDRE NNTQTTIKVF SPSDFRLEPP AKAWQQLPG

UniProtKB: Uncharacterized protein

-
Macromolecule #3: Fruiting body developmental protein R-like protein

MacromoleculeName: Fruiting body developmental protein R-like protein / type: protein_or_peptide / ID: 3 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Molecular weightTheoretical: 33.789074 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSNLNLFATI LTYPAPASNY RGESEENRSV IQKILKDGQK YAIISPESMR NALREMLIEL GQPNNRTRLH SEDQLAVEFK EYPNPDKFA DDFLFGYMVA QTNDAKEMKK LNRPAKRDSI FRCNMAVAVN PYKYDTVFYQ SPLNAGDSAW KNSTSSALLH R EVTHTAFQ ...String:
MSNLNLFATI LTYPAPASNY RGESEENRSV IQKILKDGQK YAIISPESMR NALREMLIEL GQPNNRTRLH SEDQLAVEFK EYPNPDKFA DDFLFGYMVA QTNDAKEMKK LNRPAKRDSI FRCNMAVAVN PYKYDTVFYQ SPLNAGDSAW KNSTSSALLH R EVTHTAFQ YPFALAGKDC AAKPEWVKAL LQAIAELNGV AGGHARAYYE FAPRSVVARL TPKLVAGYQT YGFDAEGNWL EL SRLTATD SDNLDLPANE FWLGGELVRK MDQEQKAQLE AMGAHLYANP EKLFADLADS FLGV

UniProtKB: Fruiting body developmental protein R-like protein

-
Macromolecule #8: CRISPR associated protein Cas11b

MacromoleculeName: CRISPR associated protein Cas11b / type: protein_or_peptide / ID: 8 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6714 (bacteria)
Molecular weightTheoretical: 14.5385 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MTVATTKTRE YAEIVYKIAQ GFVLSKLSSK HDLQWSKCKG NPKLEREYND KKEKVVNEAF LAIRSRTEKQ AFIDYFVSTL YPHVRQDEF VDFAQKLFQD TDEIRSLTLL ALSSQYPIKR QGETE

UniProtKB: Type I-MYXAN CRISPR-associated protein Cmx8

-
Macromolecule #4: DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')

MacromoleculeName: DNA (5'-D(P*TP*CP*CP*AP*TP*GP*TP*TP*TP*AP*TP*CP*AP*CP*C)-3')
type: dna / ID: 4 / Details: PAM proximal non target DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 4.494934 KDa
SequenceString:
(DT)(DC)(DC)(DA)(DT)(DG)(DT)(DT)(DT)(DA) (DT)(DC)(DA)(DC)(DC)

-
Macromolecule #6: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 6 / Details: Target DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.725236 KDa
SequenceString:
(DA)(DC)(DA)(DC)(DA)(DA)(DA)(DA)(DT)(DA) (DT)(DC)(DC)(DA)(DG)(DA)(DT)(DT)(DG)(DG) (DG)(DG)(DA)(DC)(DA)(DC)(DG)(DG)(DT) (DG)(DA)(DT)(DA)(DA)(DA)(DC)(DA)(DT)(DG) (DG) (DA)

-
Macromolecule #7: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')

MacromoleculeName: DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3') / type: dna / ID: 7 / Details: PAM distal non target DNA / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 3.08711 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)

-
Macromolecule #5: RNA (44-MER)

MacromoleculeName: RNA (44-MER) / type: rna / ID: 5 / Details: CRISPR RNA / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.975212 KDa
SequenceString:
AGAGCACUUU UAUCACCGUG UCCCCAAUCU GGAUAUUUUG UGUG

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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 / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 92454

+
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