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- EMDB-33433: Structure of Craspase-CTR -

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Basic information

Entry
Database: EMDB / ID: EMD-33433
TitleStructure of Craspase-CTR
Map data
Sample
  • Complex: Craspase-CTR complex
    • Complex: CHAT domain protein
      • Protein or peptide: CHAT domain protein
      • Protein or peptide: RAMP superfamily protein
    • Complex: RNA
      • RNA: RNA (5'-R(P*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*GP*AP*U)-3')
    • Complex: RNA 34-mer
      • RNA: RNA (34-MER)
  • Ligand: ZINC ION
KeywordsIMMUNE SYSTEM-RNA complex
Function / homologyCHAT domain / CHAT domain / : / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA binding / RAMP superfamily protein / CHAT domain protein
Function and homology information
Biological speciesCandidatus Scalindua brodae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsFeng Y / Zhang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32171274 China
CitationJournal: Mol Cell / Year: 2022
Title: Target RNA activates the protease activity of Craspase to confer antiviral defense.
Authors: Xi Liu / Laixing Zhang / Hao Wang / Yu Xiu / Ling Huang / Zhengyu Gao / Ningning Li / Feixue Li / Weijia Xiong / Teng Gao / Yi Zhang / Maojun Yang / Yue Feng /
Abstract: In the type III-E CRISPR-Cas system, a Cas effector (gRAMP) is associated with a TPR-CHAT to form Craspase (CRISPR-guided caspase). However, both the structural features of gRAMP and the immunity ...In the type III-E CRISPR-Cas system, a Cas effector (gRAMP) is associated with a TPR-CHAT to form Craspase (CRISPR-guided caspase). However, both the structural features of gRAMP and the immunity mechanism remain unknown for this system. Here, we report structures of gRAMP-crRNA and gRAMP:cRNA:target RNA as well as structures of Craspase and Craspase complexed with cognate target RNA (CTR) or non-cognate target RNA (NTR). Importantly, the 3' anti-tag region of NTR and CTR binds at two distinct channels in Craspase, and CTR with a non-complementary 3' anti-tag induces a marked conformational change of the TPR-CHAT, which allosterically activates its protease activity to cleave an ancillary protein Csx30. This cleavage then triggers an abortive infection as the antiviral strategy of the type III-E system. Together, our study provides crucial insights into both the catalytic mechanism of the gRAMP and the immunity mechanism of the type III-E system.
History
DepositionMay 15, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33433.png

Downloads & links

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Map

FileDownload / File: emd_33433.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 280 pix.
= 271.6 Å		0.97 Å/pix.
x 280 pix.
= 271.6 Å		0.97 Å/pix.
x 280 pix.
= 271.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.022
Minimum - Maximum-0.06840701 - 2.3120873
Average (Standard dev.)0.0025208904 (±0.037333716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 271.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33433_msk_1.map
Projections & Slices
AxesZYX

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Additional map: #1

Fileemd_33433_additional_1.map
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Half map: #1

Fileemd_33433_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_33433_half_map_2.map
Projections & Slices
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Sample components

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Entire : Craspase-CTR complex

EntireName: Craspase-CTR complex
Components
  • Complex: Craspase-CTR complex
    • Complex: CHAT domain protein
      • Protein or peptide: CHAT domain protein
      • Protein or peptide: RAMP superfamily protein
    • Complex: RNA
      • RNA: RNA (5'-R(P*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*GP*AP*U)-3')
    • Complex: RNA 34-mer
      • RNA: RNA (34-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Craspase-CTR complex

SupramoleculeName: Craspase-CTR complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)

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Supramolecule #2: CHAT domain protein

SupramoleculeName: CHAT domain protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)

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Supramolecule #3: RNA

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

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Supramolecule #4: RNA 34-mer

SupramoleculeName: RNA 34-mer / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

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Macromolecule #1: CHAT domain protein

MacromoleculeName: CHAT domain protein / type: protein_or_peptide / ID: 1
Details: Using a different transcription start point, the protein has additional five residues in its N-terminus.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 82.549992 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 GFPL

UniProtKB: CHAT domain protein

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Macromolecule #4: RAMP superfamily protein

MacromoleculeName: RAMP superfamily protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 197.823797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKSNDMNITV ELTFFEPYRL VEWFDWDARK KSHSAMRGQA FAQWTWKGKG RTAGKSFITG TLVRSAVIKA VEELLSLNNG KWEGVPCCN GSFQTDESKG KKPSFLRKRH TLQWQANNKN ICDKEEACPF CILLGRFDNA GKVHERNKDY DIHFSNFDLD H KQEKNDLR ...String:
MKSNDMNITV ELTFFEPYRL VEWFDWDARK KSHSAMRGQA FAQWTWKGKG RTAGKSFITG TLVRSAVIKA VEELLSLNNG KWEGVPCCN GSFQTDESKG KKPSFLRKRH TLQWQANNKN ICDKEEACPF CILLGRFDNA GKVHERNKDY DIHFSNFDLD H KQEKNDLR LVDIASGRIL NRVDFDTGKA KDYFRTWEAD YETYGTYTGR ITLRNEHAKK LLLASLGFVD KLCGALCRIE VI KKSESPL PSDTKEQSYT KDDTVEVLSE DHNDELRKQA EVIVEAFKQN DKLEKIRILA DAIRTLRLHG EGVIEKDELP DGK EERDKG HHLWDIKVQG TALRTKLKEL WQSNKDIGWR KFTEMLGSNL YLIYKKETGG VSTRFRILGD TEYYSKAHDS EGSD LFIPV TPPEGIETKE WIIVGRLKAA TPFYFGVQQP SDSIPGKEKK SEDSLVINEH TSFNILLDKE NRYRIPRSAL RGALR RDLR TAFGSGCNVS LGGQILCNCK VCIEMRRITL KDSVSDFSEP PEIRYRIAKN PGTATVEDGS LFDIEVGPEG LTFPFV LRY RGHKFPEQLS SVIRYWEEND GKNGMAWLGG LDSTGKGRFA LKDIKIFEWD LNQKINEYIK ERGMRGKEKE LLEMGES SL PDGLIPYKFF EERECLFPYK ENLKPQWSEV QYTIEVGSPL LTADTISALT EPGNRDAIAY KKRVYNDGNN AIEPEPRF A VKSETHRGIF RTAVGRRTGD LGKEDHEDCT CDMCIIFGNE HESSKIRFED LELINGNEFE KLEKHIDHVA IDRFTGGAL DKAKFDTYPL AGSPKKPLKL KGRFWIKKGF SGDHKLLITT ALSDIRDGLY PLGSKGGVGY GWVAGISIDD NVPDDFKEMI NKTEMPLPE EVEESNNGPI NNDYVHPGHQ SPKQDHKNKN IYYPHYFLDS GSKVYREKDI ITHEEFTEEL LSGKINCKLE T LTPLIIPD TSDENGLKLQ GNKPGHKNYK FFNINGELMI PGSELRGMLR THFEALTKSC FAIFGEDSTL SWRMNADEKD YK IDSNSIR KMESQRNPKY RIPDELQKEL RNSGNGLFNR LYTSERRFWS DVSNKFENSI DYKREILRCA GRPKNYKGGI IRQ RKDSLM AEELKVHRLP LYDNFDIPDS AYKANDHCRK SATCSTSRGC RERFTCGIKV RDKNRVFLNA ANNNRQYLNN IKKS NHDLY LQYLKGEKKI RFNSKVITGS ERSPIDVIAE LNERGRQTGF IKLSGLNNSN KSQGNTGTTF NSGWDRFELN ILLDD LETR PSKSDYPRPR LLFTKDQYEY NITKRCERVF EIDKGNKTGY PVDDQIKKNY EDILDSYDGI KDQEVAERFD TFTRGS KLK VGDLVYFHID GDNKIDSLIP VRISRKCASK TLGGKLDKAL HPCTGLSDGL CPGCHLFGTT DYKGRVKFGF AKYENGP EW LITRGNNPER SLTLGVLESP RPAFSIPDDE SEIPGRKFYL HHNGWRIIRQ KQLEIRETVQ PERNVTTEVM DKGNVFSF D VRFENLREWE LGLLLQSLDP GKNIAHKLGK GKPYGFGSVK IKIDSLHTFK INSNNDKIKR VPQSDIREYI NKGYQKLIE WSGNNSIQKG NVLPQWHVIP HIDKLYKLLW VPFLNDSKLE PDVRYPVLNE ESKGYIEGSD YTYKKLGDKD NLPYKTRVKG LTTPWSPWN PFQVIAEHEE QEVNVTGSRP SVTDKIERDG KMV

UniProtKB: RAMP superfamily protein

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Macromolecule #2: RNA (5'-R(P*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*GP...

MacromoleculeName: RNA (5'-R(P*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*AP*CP*GP*AP*U)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 14.898929 KDa
SequenceString:
CUCUAGUAAC AGCCGUGGAG UCCGGGGCAG AAAAUUGGAC GAUUAA

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Macromolecule #3: RNA (34-MER)

MacromoleculeName: RNA (34-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 23.741119 KDa
SequenceString:
GUUAUGAAAC AAGAGAAGGA CUUAAUGUCA CGGUACCCAA UUUUCUGCCC CGGACUCCAC GGCUGUUACU AGAG

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Macromolecule #5: ZINC ION

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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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: OTHER / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.7 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49880
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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