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Open data
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Basic information
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Title | Staphylococcus epidermidis RP62a CRISPR tall effector complex | |||||||||||||||
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Function / homology | ![]() exonuclease activity / endonuclease activity / defense response to virus / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.45 Å | |||||||||||||||
![]() | Smith EM / Ferrell SH / Tokars VL / Mondragon A | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of an active type III-A CRISPR effector complex. Authors: Eric M Smith / Sé Ferrell / Valerie L Tokars / Alfonso Mondragón / ![]() Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) provide many prokaryotes with an adaptive immune system against invading genetic material. ...Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) provide many prokaryotes with an adaptive immune system against invading genetic material. Type III CRISPR systems are unique in that they can degrade both RNA and DNA. In response to invading nucleic acids, they produce cyclic oligoadenylates that act as secondary messengers, activating cellular nucleases that aid in the immune response. Here, we present seven single-particle cryo-EM structures of the type III-A Staphylococcus epidermidis CRISPR effector complex. The structures reveal the intact S. epidermidis effector complex in an apo, ATP-bound, cognate target RNA-bound, and non-cognate target RNA-bound states and illustrate how the effector complex binds and presents crRNA. The complexes bound to target RNA capture the type III-A effector complex in a post-RNA cleavage state. The ATP-bound structures give details about how ATP binds to Cas10 to facilitate cyclic oligoadenylate production. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 17.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 25.4 KB 25.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 7.2 KB | Display | ![]() |
Images | ![]() | 69.6 KB | ||
Masks | ![]() | 34.3 MB | ![]() | |
Others | ![]() ![]() | 31.9 MB 31.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7uzzMC ![]() 7uzwC ![]() 7uzxC ![]() 7uzyC ![]() 7v00C ![]() 7v01C ![]() 7v02C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 2.1382 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #2
File | emd_26923_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26923_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Staphylococcus epidermidis RP62a CRISPR tall effector complex
Entire | Name: Staphylococcus epidermidis RP62a CRISPR tall effector complex |
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Components |
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-Supramolecule #1: Staphylococcus epidermidis RP62a CRISPR tall effector complex
Supramolecule | Name: Staphylococcus epidermidis RP62a CRISPR tall effector complex type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: RNA (37-MER)
Macromolecule | Name: RNA (37-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.895168 KDa |
Sequence | String: ACGAGAACAC GUAUGCCGAA GUAUAUAAAU CAUCAGU |
-Macromolecule #2: CRISPR system Cms protein Csm2
Macromolecule | Name: CRISPR system Cms protein Csm2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.436794 KDa |
Sequence | String: MTFAHEVVKS NVKNVKDRKG KEKQVLFNGL TTSKLRNLME QVNRLYTIAF NSNEDQLNEE FIDELEYLKI KFYYEAGREK SVDEFLKKT LMFPIIDRVI KKESKKFFLD YCKYFEALVA YAKYYQKED |
-Macromolecule #3: CRISPR system Cms protein Csm5
Macromolecule | Name: CRISPR system Cms protein Csm5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 39.449125 KDa |
Sequence | String: MTIKNYEVVI KTLGPIHIGS GQVMKKQDYI YDFYNSKVYM INGNKLVKFL KRKNLLYTYQ NFLRYPPKNP RENGLKDYLD AQNVKQSEW EAFVSYSEKV NQGKKYGNTR PKPLNDLHLM VRDGQNKVYL PGSSIKGAIK TTLVSKYNNE KNKDIYSKIK V SDSKPIDE ...String: MTIKNYEVVI KTLGPIHIGS GQVMKKQDYI YDFYNSKVYM INGNKLVKFL KRKNLLYTYQ NFLRYPPKNP RENGLKDYLD AQNVKQSEW EAFVSYSEKV NQGKKYGNTR PKPLNDLHLM VRDGQNKVYL PGSSIKGAIK TTLVSKYNNE KNKDIYSKIK V SDSKPIDE SNLAIYQKID INKSEKSMPL YRECIDVNTE IKFKLTIEDE IYSINEIEQS IQDFYKNYYD KWLVGFKETK GG RRFALEG GIPDVLNQNI LFLGAGTGFV SKTTHYQLKN RKQAKQDSFE ILTKKFRGTY GKMKEIPSNV PVALKGTTNQ SRH TSYQQG MCKVSFQELN NEVL |
-Macromolecule #4: CRISPR system Cms endoribonuclease Csm3
Macromolecule | Name: CRISPR system Cms endoribonuclease Csm3 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 24.033975 KDa |
Sequence | String: MYSKIKISGT IEVVTGLHIG GGGESSMIGA IDSPVVRDLQ TKLPIIPGSS IKGKMRNLLA KHFGLKMKQE SHNQDDERVL RLFGSSEKG NIQRARLQIS DAFFSEKTKE HFAQNDIAYT ETKFENTINR LTAVANPRQI ERVTRGSEFD FVFIYNVDEE S QVEDDFEN ...String: MYSKIKISGT IEVVTGLHIG GGGESSMIGA IDSPVVRDLQ TKLPIIPGSS IKGKMRNLLA KHFGLKMKQE SHNQDDERVL RLFGSSEKG NIQRARLQIS DAFFSEKTKE HFAQNDIAYT ETKFENTINR LTAVANPRQI ERVTRGSEFD FVFIYNVDEE S QVEDDFEN IEKAIHLLEN DYLGGGGTRG NGRIQFKDTN IETVVGEYDS TNLKIK |
-Macromolecule #5: CRISPR system Cms protein Csm4
Macromolecule | Name: CRISPR system Cms protein Csm4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.551938 KDa |
Sequence | String: MTLATKVFKL SFKTPVHFGK KRLSDGEMTI TADTLFSALF IETLQLGKDT DWLLNDLIIS DTFPYENELY YLPKPLIKID SKEEDNHKA FKKLKYVPVH HYNQYLNGEL SAEDATDLND IFNIGYFSLQ TKVSLIAQET DSSADSEPYS VGTFTFEPEA G LYFIAKGS ...String: MTLATKVFKL SFKTPVHFGK KRLSDGEMTI TADTLFSALF IETLQLGKDT DWLLNDLIIS DTFPYENELY YLPKPLIKID SKEEDNHKA FKKLKYVPVH HYNQYLNGEL SAEDATDLND IFNIGYFSLQ TKVSLIAQET DSSADSEPYS VGTFTFEPEA G LYFIAKGS EETLDHLNNI MTALQYSGLG GKRNAGYGQF EYEIINNQQL SKLLNQNGKH SILLSTAMAK KEEIESALKE AR YILTKRS GFVQSTNYSE MLVKKSDFYS FSSGSVFKNI FNGDIFNVGH NGKHPVYRYA KPLWLEV |
-Macromolecule #6: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1...
Macromolecule | Name: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 87.685781 KDa |
Sequence | String: MNKKNILMYG SLLHDIGKII YRSGDHTFSR GTHSKLGHQF LSQFSEFKDN EVLDNVAYHH YKELAKANLD NDNTAYITYI ADNIASGID RRDIIEEGDE EYEKQLFNFD KYTPLYSVFN IVNSEKLKQT NGKFKFSNES NIEYPKTENI QYSSGNYTTL M KDMSHDLE ...String: MNKKNILMYG SLLHDIGKII YRSGDHTFSR GTHSKLGHQF LSQFSEFKDN EVLDNVAYHH YKELAKANLD NDNTAYITYI ADNIASGID RRDIIEEGDE EYEKQLFNFD KYTPLYSVFN IVNSEKLKQT NGKFKFSNES NIEYPKTENI QYSSGNYTTL M KDMSHDLE HKLSIKEGTF PSLLQWTESL WQYVPSSTNK NQLIDISLYD HSRITCAIAS CIFDYLNENN IHNYKDELFS KY ENTKSFY QKEAFLLLSM DMSGIQDFIY NISGSKALKS LRSRSFYLEL MLEVIVDQLL ERLELARANL LYTGGGHAYL LVS NTDKVK KKITQFNNEL KKWFMSEFTT DLSLSMAFEK CSGDDLMNTS GNYRTIWRNV SSKLSDIKAH KYSAEDILKL NHFH SYGDR ECKECLRSDI DINDDGLCSI CEGIINISND LRDKSFFVLS ETGKLKMPFN KFISVIDYEE AEMLVQNNNQ VRIYS KNKP YIGIGISTNL WMCDYDYASQ NQDMREKGIG SYVDREEGVK RLGVVRADID NLGATFISGI PEKYNSISRT ATLSRQ LSL FFKYELNHLL ENYQITAIYS GGDDLFLIGA WDDIIEASIY INDKFKEFTL DKLTLSAGVG MFSGKYPVSK MAFETGR LE EAAKTGEKNQ ISLWLQEKVY NWDEFKKNIL EEKLLVLQQG FSQTDEHGKA FIYKMLALLR NNEAINIARL AYLLARSK M NEDFTSKIFN WAQNDKDKNQ LITALEYYIY QIREAD |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 3.2 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Homemade / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE Details: Grids were glow discharged for 10 seconds with 12 mA current (Pelco easiGlow) prior to use on Chameleon. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: SPOTITON Details: Grids were prepared at the National Center for CryoEM Access and Training (NCCAT) using a Chameleon (SPT Labtech) blotless system. 300 mesh nanowire grids with multi-hole pattern carbon film ...Details: Grids were prepared at the National Center for CryoEM Access and Training (NCCAT) using a Chameleon (SPT Labtech) blotless system. 300 mesh nanowire grids with multi-hole pattern carbon film and a thin layer of gold coating (~ 5 nm) (SPT Labtech)were used. |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 6041 / Average electron dose: 61.07 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 46772 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |