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- EMDB-33439: Structure of Craspase-NTR -

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Basic information

Entry
Database: EMDB / ID: EMD-33439
TitleStructure of Craspase-NTR
Map data
Sample
  • Complex: Craspase-NTR complex
    • Complex: RAMP superfamily protein, 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*GP*UP*AP*CP*CP*G)-3')
    • Complex: RNA (34-MER)
      • RNA: RNA (34-MER)
  • Ligand: ZINC ION
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: 3.08 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 16, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33439.png

Downloads & links

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Map

FileDownload / File: emd_33439.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.97 Å
Density
Contour LevelBy AUTHOR: 0.056
Minimum - Maximum-0.069493 - 2.6289697
Average (Standard dev.)0.0024875714 (±0.037354942)
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_33439_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_33439_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33439_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33439_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : Craspase-NTR complex

EntireName: Craspase-NTR complex
Components
  • Complex: Craspase-NTR complex
    • Complex: RAMP superfamily protein, 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*GP*UP*AP*CP*CP*G)-3')
    • Complex: RNA (34-MER)
      • RNA: RNA (34-MER)
  • Ligand: ZINC ION

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Supramolecule #1: Craspase-NTR complex

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

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Supramolecule #2: RAMP superfamily protein, CHAT domain protein

SupramoleculeName: RAMP superfamily protein, CHAT domain protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3

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Supramolecule #3: RNA

SupramoleculeName: RNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)

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Supramolecule #4: RNA (34-MER)

SupramoleculeName: RNA (34-MER) / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4

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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

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Macromolecule #3: RAMP superfamily protein

MacromoleculeName: RAMP superfamily protein / type: protein_or_peptide / ID: 3 / 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

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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*GP*UP*AP...

MacromoleculeName: RNA (5'-R(P*GP*GP*GP*GP*CP*AP*GP*AP*AP*AP*AP*UP*UP*GP*GP*GP*UP*AP*CP*CP*G)-3')
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 14.906905 KDa
SequenceString:
CUCUAGUAAC AGCCGUGGAG UCCGGGGCAG AAAAUUGGGU ACCGUG

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Macromolecule #4: RNA (34-MER)

MacromoleculeName: RNA (34-MER) / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Candidatus Scalindua brodae (bacteria)
Molecular weightTheoretical: 17.828559 KDa
SequenceString:
GACUUAAUGU CACGGUACCC AAUUUUCUGC CCCGGACUCC ACGGCUGUUA CUAGAG

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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
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
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40262
FSC plot (resolution estimation)

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