[English] 日本語
Yorodumi
- EMDB-37649: Cryo-EM structure of DiCas7-11-crRNA in complex with regulator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-37649
TitleCryo-EM structure of DiCas7-11-crRNA in complex with regulator
Map data
Sample
  • Complex: Ternary complex of Cas7-11_crRNA_TPR-CHAT
    • Protein or peptide: CRISPR-associated RAMP family protein
    • Protein or peptide: CHAT domain-containing protein
    • RNA: RNA (38-MER)
  • Ligand: ZINC ION
KeywordsCRISPR-Cas / Gene editing / TPR-CHAT / IMMUNE SYSTEM
Function / homologyCHAT domain / CHAT domain / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / CRISPR-associated RAMP family protein / CHAT domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli) / Desulfonema ishimotonii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsMa HY / Tang XD
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)81971974 China
Ministry of Science and Technology (MoST, China)32222040 China
CitationJournal: Signal Transduct Target Ther / Year: 2024
Title: Structural basis of negative regulation of CRISPR-Cas7-11 by TPR-CHAT.
Authors: Tian Hong / Qinghua Luo / Haiyun Ma / Xin Wang / Xinqiong Li / Chongrong Shen / Jie Pang / Yan Wang / Yuejia Chen / Changbin Zhang / Zhaoming Su / Haohao Dong / Xiaodi Tang /
Abstract: CRISPR‒Cas7-11 is a Type III-E CRISPR-associated nuclease that functions as a potent RNA editing tool. Tetratrico-peptide repeat fused with Cas/HEF1-associated signal transducer (TPR-CHAT) acts as ...CRISPR‒Cas7-11 is a Type III-E CRISPR-associated nuclease that functions as a potent RNA editing tool. Tetratrico-peptide repeat fused with Cas/HEF1-associated signal transducer (TPR-CHAT) acts as a regulatory protein that interacts with CRISPR RNA (crRNA)-bound Cas7-11 to form a CRISPR-guided caspase complex (Craspase). However, the precise modulation of Cas7-11's nuclease activity by TPR-CHAT to enhance its utility requires further study. Here, we report cryo-electron microscopy (cryo-EM) structures of Desulfonema ishimotonii (Di) Cas7-11-crRNA, complexed with or without the full length or the N-terminus of TPR-CHAT. These structures unveil the molecular features of the Craspase complex. Structural analysis, combined with in vitro nuclease assay and electrophoretic mobility shift assay, reveals that DiTPR-CHAT negatively regulates the activity of DiCas7-11 by preventing target RNA from binding through the N-terminal 65 amino acids of DiTPR-CHAT (DiTPR-CHAT). Our work demonstrates that DiTPR-CHAT can function as a small unit of DiCas7-11 regulator, potentially enabling safe applications to prevent overcutting and off-target effects of the CRISPR‒Cas7-11 system.
History
DepositionOct 3, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_37649.png

Downloads & links

-
Map

FileDownload / File: emd_37649.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.81610924 - 1.6282938
Average (Standard dev.)0.0008173502 (±0.040644377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_37649_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_37649_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_37649_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of Cas7-11_crRNA_TPR-CHAT

EntireName: Ternary complex of Cas7-11_crRNA_TPR-CHAT
Components
  • Complex: Ternary complex of Cas7-11_crRNA_TPR-CHAT
    • Protein or peptide: CRISPR-associated RAMP family protein
    • Protein or peptide: CHAT domain-containing protein
    • RNA: RNA (38-MER)
  • Ligand: ZINC ION

-
Supramolecule #1: Ternary complex of Cas7-11_crRNA_TPR-CHAT

SupramoleculeName: Ternary complex of Cas7-11_crRNA_TPR-CHAT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #3
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: CHAT domain-containing protein

MacromoleculeName: CHAT domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Desulfonema ishimotonii (bacteria)
Molecular weightTheoretical: 88.311875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNPIRDIQD RLKTAKFDNK DDMMNLASSL YKYEKQLMDS SEATLCQQGL SNRPNSFSQL SQFRDSDIQS KAGGQTGKFW QNEYEACKN FQTHKERRET LEQIIRFLQN GAEEKDADDL LLKTLARAYF HRGLLYRPKG FSVPARKVEA MKKAIAYCEI I LDKNEEES ...String:
MSNPIRDIQD RLKTAKFDNK DDMMNLASSL YKYEKQLMDS SEATLCQQGL SNRPNSFSQL SQFRDSDIQS KAGGQTGKFW QNEYEACKN FQTHKERRET LEQIIRFLQN GAEEKDADDL LLKTLARAYF HRGLLYRPKG FSVPARKVEA MKKAIAYCEI I LDKNEEES EALRIWLYAA MELRRCGEEY PENFAEKLFY LANDGFISEL YDIRLFLEYT EREEDNNFLD MILQENQDRE RL FELCLYK ARACFHLNQL NDVRIYGESA IDNAPGAFAD PFWDELVEFI RMLRNKKSEL WKEIAIKAWD KCREKEMKVG NNI YLSWYW ARQRELYDLA FMAQDGIEKK TRIADSLKSR TTLRIQELNE LRKDAHRKQN RRLEDKLDRI IEQENEARDG AYLR RNPPC FTGGKREEIP FARLPQNWIA VHFYLNELES HEGGKGGHAL IYDPQKAEKD QWQDKSFDYK ELHRKFLEWQ ENYIL NEEG SADFLVTLCR EIEKAMPFLF KSEVIPEDRP VLWIPHGFLH RLPLHAAMKS GNNSNIEIFW ERHASRYLPA WHLFDP APY SREESSTLLK NFEEYDFQNL ENGEIEVYAP SSPKKVKEAI RENPAILLLL CHGEADMTNP FRSCLKLKNK DMTIFDL LT VEDVRLSGSR ILLGACESDM VPPLEFSVDE HLSVSGAFLS HKAGEIVAGL WTVDSEKVDE CYSYLVEEKD FLRNLQEW Q MAETENFRSE NDSSLFYKIA PFRIIGFPAE

UniProtKB: CHAT domain-containing protein

-
Macromolecule #2: CRISPR-associated RAMP family protein

MacromoleculeName: CRISPR-associated RAMP family protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Desulfonema ishimotonii (bacteria)
Molecular weightTheoretical: 183.933 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTTMKISIE FLEPFRMTKW QESTRRNKNN KEFVRGQAFA RWHRNKKDNT KGRPYITGTL LRSAVIRSAE NLLTLSDGKI SEKTCCPGK FDTEDKDRLL QLRQRSTLRW TDKNPCPDNA ETYCPFCELL GRSGNDGKKA EKKDWRFRIH FGNLSLPGKP D FDGPKAIG ...String:
MTTTMKISIE FLEPFRMTKW QESTRRNKNN KEFVRGQAFA RWHRNKKDNT KGRPYITGTL LRSAVIRSAE NLLTLSDGKI SEKTCCPGK FDTEDKDRLL QLRQRSTLRW TDKNPCPDNA ETYCPFCELL GRSGNDGKKA EKKDWRFRIH FGNLSLPGKP D FDGPKAIG SQRVLNRVDF KSGKAHDFFK AYEVDHTRFP RFEGEITIDN KVSAEARKLL CDSLKFTDRL CGALCVIRFD EY TPAADSG KQTENVQAEP NANLAEKTAE QIISILDDNK KTEYTRLLAD AIRSLRRSSK LVAGLPKDHD GKDDHYLWDI GKK KKDENS VTIRQILTTS ADTKELKNAG KWREFCEKLG EALYLKSKDM SGGLKITRRI LGDAEFHGKP DRLEKSRSVS IGSV LKETV VCGELVAKTP FFFGAIDEDA KQTDLQVLLT PDNKYRLPRS AVRGILRRDL QTYFDSPCNA ELGGRPCMCK TCRIM RGIT VMDARSEYNA PPEIRHRTRI NPFTGTVAEG ALFNMEVAPE GIVFPFQLRY RGSEDGLPDA LKTVLKWWAE GQAFMS GAA STGKGRFRME NAKYETLDLS DENQRNDYLK NWGWRDEKGL EELKKRLNSG LPEPGNYRDP KWHEINVSIE MASPFIN GD PIRAAVDKRG TDVVTFVKYK AEGEEAKPVC AYKAESFRGV IRSAVARIHM EDGVPLTELT HSDCECLLCQ IFGSEYEA G KIRFEDLVFE SDPEPVTFDH VAIDRFTGGA ADKKKFDDSP LPGSPARPLM LKGSFWIRRD VLEDEEYCKA LGKALADVN NGLYPLGGKS AIGYGQVKSL GIKGDDKRIS RLMNPAFDET DVAVPEKPKT DAEVRIEAEK VYYPHYFVEP HKKVEREEKP CGHQKFHEG RLTGKIRCKL ITKTPLIVPD TSNDDFFRPA DKEARKEKDE YHKSYAFFRL HKQIMIPGSE LRGMVSSVYE T VTNSCFRI FDETKRLSWR MDADHQNVLQ DFLPGRVTAD GKHIQKFSET ARVPFYDKTQ KHFDILDEQE IAGEKPVRMW VK RFIKRLS LVDPAKHPQK KQDNKWKRRK EGIATFIEQK NGSYYFNVVT NNGCTSFHLW HKPDNFDQEK LEGIQNGEKL DCW VRDSRY QKAFQEIPEN DPDGWECKEG YLHVVGPSKV EFSDKKGDVI NNFQGTLPSV PNDWKTIRTN DFKNRKRKNE PVFC CEDDK GNYYTMAKYC ETFFFDLKEN EEYEIPEKAR IKYKELLRVY NNNPQAVPES VFQSRVAREN VEKLKSGDLV YFKHN EKYV EDIVPVRISR TVDDRMIGKR MSADLRPCHG DWVEDGDLSA LNAYPEKRLL LRHPKGLCPA CRLFGTGSYK GRVRFG FAS LENDPEWLIP GKNPGDPFHG GPVMLSLLER PRPTWSIPGS DNKFKVPGRK FYVHHHAWKT IKDGNHPTTG KAIEQSP NN RTVEALAGGN SFSFEIAFEN LKEWELGLLI HSLQLEKGLA HKLGMAKSMG FGSVEIDVES VRLRKDWKQW RNGNSEIP N WLGKGFAKLK EWFRDELDFI ENLKKLLWFP EGDQAPRVCY PMLRKKDDPN GNSGYEELKD GEFKKEDRQK KLTTPWTPW A

UniProtKB: CRISPR-associated RAMP family protein

-
Macromolecule #3: RNA (38-MER)

MacromoleculeName: RNA (38-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 12.134133 KDa
SequenceString:
UUGAUGUCAC GGAACCUUUG UUGUCUUCGA CAUGGGUA

-
Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

Concentration0.8 mg/mL
BufferpH: 8
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 53.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.96 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78984
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://pdbjlvh1.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