+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33114 | |||||||||
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Title | Cryo-EM structure of a bacterial protein complex | |||||||||
Map data | main map sharpended using deepEMhancer | |||||||||
Sample |
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Keywords | Complex / RNA-binding / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | CHAT domain / CHAT domain / CHAT domain protein Function and homology information | |||||||||
Biological species | Candidatus Scalindua brodae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Yu G / Wang X / Deng Z / Zhang H | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Microbiol / Year: 2022 Title: Structure and function of a bacterial type III-E CRISPR-Cas7-11 complex. Authors: Guimei Yu / Xiaoshen Wang / Yi Zhang / Qiyin An / Yanan Wen / Xuzichao Li / Hang Yin / Zengqin Deng / Heng Zhang / Abstract: The type III-E CRISPR-Cas system uses a single multidomain effector called Cas7-11 (also named gRAMP) to cleave RNA and associate with a caspase-like protease Csx29, showing promising potential for ...The type III-E CRISPR-Cas system uses a single multidomain effector called Cas7-11 (also named gRAMP) to cleave RNA and associate with a caspase-like protease Csx29, showing promising potential for RNA-targeting applications. The structural and molecular mechanisms of the type III-E CRISPR-Cas system remain poorly understood. Here we report four cryo-electron microscopy structures of Cas7-11 at different functional states. Cas7-11 has four Cas7-like domains, which assemble into a helical filament to accommodate CRISPR RNA (crRNA), and a Cas11-like domain facilitating crRNA-target RNA duplex formation. The Cas7.1 domain is critical for crRNA maturation, whereas Cas7.2 and Cas7.3 are responsible for target RNA cleavage. Target RNA binding induces the structural arrangements of Csx29, potentially exposing the catalytic site of Csx29. These results delineate the molecular mechanisms underlying pre-crRNA processing, target RNA recognition and cleavage for Cas7-11, and provide a structural framework to understand the role of Csx29 in type III-E CRISPR system. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33114.map.gz | 91.6 MB | EMDB map data format | |
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Header (meta data) | emd-33114-v30.xml emd-33114.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33114_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_33114.png | 123 KB | ||
Filedesc metadata | emd-33114.cif.gz | 7.3 KB | ||
Others | emd_33114_half_map_1.map.gz emd_33114_half_map_2.map.gz | 95.7 MB 95.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33114 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33114 | HTTPS FTP |
-Validation report
Summary document | emd_33114_validation.pdf.gz | 852.9 KB | Display | EMDB validaton report |
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Full document | emd_33114_full_validation.pdf.gz | 852.5 KB | Display | |
Data in XML | emd_33114_validation.xml.gz | 18 KB | Display | |
Data in CIF | emd_33114_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33114 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33114 | HTTPS FTP |
-Related structure data
Related structure data | 7xc7MC 7x7aC 7x7rC 7x8aC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33114.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | main map sharpended using deepEMhancer | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.95 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: unmasked
File | emd_33114_half_map_1.map | ||||||||||||
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Annotation | unmasked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unmasked
File | emd_33114_half_map_2.map | ||||||||||||
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Annotation | unmasked | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : quaternary complex
Entire | Name: quaternary complex |
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Components |
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-Supramolecule #1: quaternary complex
Supramolecule | Name: quaternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
-Macromolecule #1: CHAT domain protein
Macromolecule | Name: CHAT domain protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 82.549992 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 |
-Macromolecule #4: RAMP superfamily protein
Macromolecule | Name: RAMP superfamily protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 197.749766 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: 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 ASFNILLDKE 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 EPGNRAAIAY 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 |
-Macromolecule #2: RNA (33-MER)
Macromolecule | Name: RNA (33-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 10.404171 KDa |
Sequence | String: GACUUAAUGU CACGGUACCC AAUUUUCUGC CCC |
-Macromolecule #3: RNA (46-mer)
Macromolecule | Name: RNA (46-mer) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: Candidatus Scalindua brodae (bacteria) |
Molecular weight | Theoretical: 14.898929 KDa |
Sequence | String: CUCUAGUAAC AGCCGUGGAG UCCGGGGCAG AAAAUUGGAC GAUUAA |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.6 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
Details | No further treatment. |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |