[English] 日本語
Yorodumi
- EMDB-33679: CryoEM structure of type III-E CRISPR gRAMP-crRNA in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-33679
TitleCryoEM structure of type III-E CRISPR gRAMP-crRNA in complex with TPR-CHAT bound to non-self RNA target
Map data
Sample
  • Complex: Type III-E CRISPR gRAMP-crRNA binary complex
    • Complex: gRAMP
      • Protein or peptide: RAMP superfamily protein
    • Complex: crRNA
      • RNA: crRNA
    • Complex: Non-self RNA target
      • RNA: non-self RNA
    • Complex: TPR-CHAT
      • Protein or peptide: CHAT domain protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsNuclease / STRUCTURAL PROTEIN-RNA COMPLEX
Function / homologyCHAT domain / CHAT domain / : / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RAMP superfamily protein / CHAT domain protein
Function and homology information
Biological speciesCandidatus Scalindua brodae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsZhang JT / Cui N / Huang HD / Jia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for the non-self RNA-activated protease activity of the type III-E CRISPR nuclease-protease Craspase.
Authors: Ning Cui / Jun-Tao Zhang / Zhuolin Li / Xiao-Yu Liu / Chongyuan Wang / Hongda Huang / Ning Jia /
Abstract: The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. ...The RNA-targeting type III-E CRISPR-gRAMP effector interacts with a caspase-like protease TPR-CHAT to form the CRISPR-guided caspase complex (Craspase), but their functional mechanism is unknown. Here, we report cryo-EM structures of the type III-E gRAMP and gRAMP-TPR-CHAT complexes, before and after either self or non-self RNA target binding, and elucidate the mechanisms underlying RNA-targeting and non-self RNA-induced protease activation. The associated TPR-CHAT adopted a distinct conformation upon self versus non-self RNA target binding, with nucleotides at positions -1 and -2 of the CRISPR-derived RNA (crRNA) serving as a sensor. Only binding of the non-self RNA target activated the TPR-CHAT protease, leading to cleavage of Csx30 protein. Furthermore, TPR-CHAT structurally resembled eukaryotic separase, but with a distinct mechanism for protease regulation. Our findings should facilitate the development of gRAMP-based RNA manipulation tools, and advance our understanding of the virus-host discrimination process governed by a nuclease-protease Craspase during type III-E CRISPR-Cas immunity.
History
DepositionJun 22, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_33679.png

Downloads & links

-
Map

FileDownload / File: emd_33679.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 Å		1.1 Å/pix.
x 256 pix.
= 281.6 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: 1.0
Minimum - Maximum-4.5766926 - 8.206773
Average (Standard dev.)0.00015022374 (±0.19419788)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_33679_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_33679_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_33679_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Type III-E CRISPR gRAMP-crRNA binary complex

EntireName: Type III-E CRISPR gRAMP-crRNA binary complex
Components
  • Complex: Type III-E CRISPR gRAMP-crRNA binary complex
    • Complex: gRAMP
      • Protein or peptide: RAMP superfamily protein
    • Complex: crRNA
      • RNA: crRNA
    • Complex: Non-self RNA target
      • RNA: non-self RNA
    • Complex: TPR-CHAT
      • Protein or peptide: CHAT domain protein
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

+
Supramolecule #1: Type III-E CRISPR gRAMP-crRNA binary complex

SupramoleculeName: Type III-E CRISPR gRAMP-crRNA binary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)

+
Supramolecule #2: gRAMP

SupramoleculeName: gRAMP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)

+
Supramolecule #3: crRNA

SupramoleculeName: crRNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

+
Supramolecule #4: Non-self RNA target

SupramoleculeName: Non-self RNA target / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Candidatus Scalindua brodae (bacteria) / Synthetically produced: Yes

+
Supramolecule #5: TPR-CHAT

SupramoleculeName: TPR-CHAT / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4

+
Macromolecule #1: RAMP superfamily protein

MacromoleculeName: RAMP superfamily protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 198.652688 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHKSN DMNITVELTF FEPYRLVEWF DWDARKKSHS AMRGQAFAQW TWKGKGRTAG KSFITGTLVR SAVIKAVEEL LSLNNGKWE GVPCCNGSFQ TDESKGKKPS FLRKRHTLQW QANNKNICDK EEACPFCILL GRFDNAGKVH ERNKDYDIHF S NFDLDHKQ ...String:
MHHHHHHKSN DMNITVELTF FEPYRLVEWF DWDARKKSHS AMRGQAFAQW TWKGKGRTAG KSFITGTLVR SAVIKAVEEL LSLNNGKWE GVPCCNGSFQ TDESKGKKPS FLRKRHTLQW QANNKNICDK EEACPFCILL GRFDNAGKVH ERNKDYDIHF S NFDLDHKQ EKNDLRLVDI ASGRILNRVD FDTGKAKDYF RTWEADYETY GTYTGRITLR NEHAKKLLLA SLGFVDKLCG AL CRIEVIK KSESPLPSDT KEQSYTKDDT VEVLSEDHND ELRKQAEVIV EAFKQNDKLE KIRILADAIR TLRLHGEGVI EKD ELPDGK EERDKGHHLW DIKVQGTALR TKLKELWQSN KDIGWRKFTE MLGSNLYLIY KKETGGVSTR FRILGDTEYY SKAH DSEGS DLFIPVTPPE GIETKEWIIV GRLKAATPFY FGVQQPSDSI PGKEKKSEDS LVINEHTSFN ILLDKENRYR IPRSA LRGA LRRDLRTAFG SGCNVSLGGQ ILCNCKVCIE MRRITLKDSV SDFSEPPEIR YRIAKNPGTA TVEDGSLFDI EVGPEG LTF PFVLRYRGHK FPEQLSSVIR YWEENDGKNG MAWLGGLDST GKGRFALKDI KIFEWDLNQK INEYIKERGM RGKEKEL LE MGESSLPDGL IPYKFFEERE CLFPYKENLK PQWSEVQYTI EVGSPLLTAD TISALTEPGN RDAIAYKKRV YNDGNNAI E PEPRFAVKSE THRGIFRTAV GRRTGDLGKE DHEDCTCDMC IIFGNEHESS KIRFEDLELI NGNEFEKLEK HIDHVAIDR FTGGALDKAK FDTYPLAGSP KKPLKLKGRF WIKKGFSGDH KLLITTALSD IRDGLYPLGS KGGVGYGWVA GISIDDNVPD DFKEMINKT EMPLPEEVEE SNNGPINNDY VHPGHQSPKQ DHKNKNIYYP HYFLDSGSKV YREKDIITHE EFTEELLSGK I NCKLETLT PLIIPDTSDE NGLKLQGNKP GHKNYKFFNI NGELMIPGSE LRGMLRTHFE ALTKSCFAIF GEDSTLSWRM NA DEKDYKI DSNSIRKMES QRNPKYRIPD ELQKELRNSG NGLFNRLYTS ERRFWSDVSN KFENSIDYKR EILRCAGRPK NYK GGIIRQ RKDSLMAEEL KVHRLPLYDN FDIPDSAYKA NDHCRKSATC STSRGCRERF TCGIKVRDKN RVFLNAANNN RQYL NNIKK SNHDLYLQYL KGEKKIRFNS KVITGSERSP IDVIAELNER GRQTGFIKLS GLNNSNKSQG NTGTTFNSGW DRFEL NILL DDLETRPSKS DYPRPRLLFT KDQYEYNITK RCERVFEIDK GNKTGYPVDD QIKKNYEDIL DSYDGIKDQE VAERFD TFT RGSKLKVGDL VYFHIDGDNK IDSLIPVRIS RKCASKTLGG KLDKALHPCT GLSDGLCPGC HLFGTTDYKG RVKFGFA KY ENGPEWLITR GNNPERSLTL GVLESPRPAF SIPDDESEIP GRKFYLHHNG WRIIRQKQLE IRETVQPERN VTTEVMDK G NVFSFDVRFE NLREWELGLL LQSLDPGKNI AHKLGKGKPY GFGSVKIKID SLHTFKINSN NDKIKRVPQS DIREYINKG YQKLIEWSGN NSIQKGNVLP QWHVIPHIDK LYKLLWVPFL NDSKLEPDVR YPVLNEESKG YIEGSDYTYK KLGDKDNLPY KTRVKGLTT PWSPWNPFQV IAEHEEQEVN VTGSRPSVTD KIERDGKMV

UniProtKB: RAMP superfamily protein

+
Macromolecule #4: CHAT domain protein

MacromoleculeName: CHAT domain protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 85.523141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNNTEENIDR IQEPTREDID RKEAERLLDE AFNPRTKPVD RKKIINSALK ILIGLYKEKK DDLTSASFIS IARAYYLVSI TILPKGTTI PEKKKEALRK GIEFIDRAIN KFNGSILDSQ RAFRIKSVLS IEFNRIDREK CDNIKLKNLL NEAVDKGCTD F DTYEWDIQ ...String:
MNNTEENIDR IQEPTREDID RKEAERLLDE AFNPRTKPVD RKKIINSALK ILIGLYKEKK DDLTSASFIS IARAYYLVSI TILPKGTTI PEKKKEALRK GIEFIDRAIN KFNGSILDSQ RAFRIKSVLS IEFNRIDREK CDNIKLKNLL NEAVDKGCTD F DTYEWDIQ IAIRLCELGV DMEGHFDNLI KSNKANDLQK AKAYYFIKKD DHKAKEHMDK CTASLKYTPC SHRLWDETVG FI ERLKGDS STLWRDFAIK TYRSCRVQEK ETGTLRLRWY WSRHRVLYDM AFLAVKEQAD DEEPDVNVKQ AKIKKLAEIS DSL KSRFSL RLSDMEKMPK SDDESNHEFK KFLDKCVTAY QDGYVINRSE DKEGQGENKS TTSKQPEPRP QAKLLELTQV PEGW VVVHF YLNKLEGMGN AIVFDKCANS WQYKEFQYKE LFEVFLTWQA NYNLYKENAA EHLVTLCKKI GETMPFLFCD NFIPN GKDV LFVPHDFLHR LPLHGSIENK TNGKLFLENH SCCYLPAWSF ASEKEASTSD EYVLLKNFDQ GHFETLQNNQ IWGTQS VKD GASSDDLENI RNNPRLLTIL CHGEANMSNP FRSMLKLANG GITYLEILNS VKGLKGSQVI LGACETDLVP PLSDVMD EH YSVATALLLI GAAGVVGTMW KVRSNKTKSL IEWKLENIEY KLNEWQKETG GAAYKDHPPT FYRSIAFRSI GFPLGGSG W SHPQFEKGGG SGGGSGGWSH PQFEK

UniProtKB: CHAT domain protein

+
Macromolecule #2: crRNA

MacromoleculeName: crRNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 35.43209 KDa
SequenceString:
GUUAUGAAAC AAGAGAAGGA CUUAAUGUCA CGGUACCCAA UUUUCUGCCC CGGACUCCAC GGCUGUUACU AGAGGUUAUG AAACAAGAG AAGGACUUAA UGUCACGGUA C

+
Macromolecule #3: non-self RNA

MacromoleculeName: non-self RNA / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 18.097797 KDa
SequenceString:
CUCUAGUAAC AGCCGUGGAG UCCGGGGCAG AAAAUUGGCA UGGCACUGUA AUUCAG

+
Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 53439
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