+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40249 | |||||||||
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Title | CRISPR-Cas type III-D effector complex bound to a target RNA | |||||||||
Map data | CRISPR-Cas type III-D complex bound to target RNA | |||||||||
Sample |
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Keywords | CRISPR / CRISPR-Cas / type III / complex / RNA / crRNA / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.77 Å | |||||||||
Authors | Schwartz EA / Taylor DW | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Type III CRISPR-Cas effectors act as protein-assisted ribozymes Authors: Schwartz EA / Bravo JPK / Ahsan F / Macias LA / Brodbelt JS / Brodbelt JS / Palermo G / Fineran PC / Fagerlund RD / Taylor DW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40249.map.gz | 286.3 MB | EMDB map data format | |
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Header (meta data) | emd-40249-v30.xml emd-40249.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40249_fsc.xml | 14.5 KB | Display | FSC data file |
Images | emd_40249.png | 45.4 KB | ||
Filedesc metadata | emd-40249.cif.gz | 8.2 KB | ||
Others | emd_40249_additional_1.map.gz emd_40249_additional_2.map.gz emd_40249_half_map_1.map.gz emd_40249_half_map_2.map.gz | 289.4 MB 289 MB 284.9 MB 285 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40249 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40249 | HTTPS FTP |
-Validation report
Summary document | emd_40249_validation.pdf.gz | 767 KB | Display | EMDB validaton report |
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Full document | emd_40249_full_validation.pdf.gz | 766.6 KB | Display | |
Data in XML | emd_40249_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | emd_40249_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40249 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40249 | HTTPS FTP |
-Related structure data
Related structure data | 8s9uMC M: atomic model generated by this map C: citing same article (ref.) |
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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_40249.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | CRISPR-Cas type III-D complex bound to target RNA | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.81 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Initial Refinement Map
File | emd_40249_additional_1.map | ||||||||||||
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Annotation | Initial Refinement Map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refinement map
File | emd_40249_additional_2.map | ||||||||||||
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Annotation | Local refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Initial refinement half map
File | emd_40249_half_map_1.map | ||||||||||||
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Annotation | Initial refinement half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Initial refinement half map
File | emd_40249_half_map_2.map | ||||||||||||
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Annotation | Initial refinement half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CRISPR-Cas type III-D effector complex bound to target RNA
Entire | Name: CRISPR-Cas type III-D effector complex bound to target RNA |
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Components |
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-Supramolecule #1: CRISPR-Cas type III-D effector complex bound to target RNA
Supramolecule | Name: CRISPR-Cas type III-D effector complex bound to target RNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 351 KDa |
-Macromolecule #1: Cas7-Cas5-Cas11
Macromolecule | Name: Cas7-Cas5-Cas11 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 87.558938 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRGIEITITM QSDWHVGTGM GRGELDSVVQ RDGDNLPYIP GKTLTGILRD SCEQVALGLD NGQTRGLWHG WINFIFGDQP ALAQGAIEP EPRPALIAIG SAHLDPKLKA AFQGKKQLQE AIAFMKPGVA IDAITGTAKK DFLRFEEVVR LGAKLTAEVE L NLPDNLSE ...String: MRGIEITITM QSDWHVGTGM GRGELDSVVQ RDGDNLPYIP GKTLTGILRD SCEQVALGLD NGQTRGLWHG WINFIFGDQP ALAQGAIEP EPRPALIAIG SAHLDPKLKA AFQGKKQLQE AIAFMKPGVA IDAITGTAKK DFLRFEEVVR LGAKLTAEVE L NLPDNLSE TNKKVIAGIL ASGAKLTERL GGKRRRGNGR CELKFSGYSD QQIQWLKDNY QSVDQPPKYQ QNKLQSAGDN PE QQPPWHI IPLTIKTLSP VVLPARTVGN VVECLDYIPG RYLLGYIHKT LGEYFDVSQA IAAGDLIITN ATIKIDGKAG RAT PFCLFG EKLDGGLGKG KGVYNRFQES EPDGIQLKGE RGGYVGQFEQ EQRNLPNTGK INSELFTHNT IQDDVQRPTS DVGG VYSYE AIIAGQTFVA ELRLPDSLVK QITSKNKNWQ AQLKATIRIG QSKKDQYGKI EVTSGNSADL PKPTGNNKTL SIWFL SDIL LRGDRLNFNA TPDDLKKYLE NALDIKLKER SDNDLICIAL RSQRTESWQV RWGLPRPSLV GWQAGSCLIY DIESGT VNA EKLQELMITG IGDRCTEGYG QIGFNDPLLS ASLGKLTAKP KASNNQSQNS QSNPLPTNHP TQDYARLIEK AAWREAI QN KALALASSRA KREEILGIKI MGKDSQPTMT QLGGFRSVLK RLHSRNNRDI VTGYLTALEQ VSNRKEKWSN TSQGLTKI R NLVTQENLIW NHLDIDFSPL TITQNGVNQL KSELWAEAVR TLVDAIIRGH KRDLEKAQEN ESNQQSQGAA UniProtKB: DUF324 domain-containing protein |
-Macromolecule #2: TIGR03984 family CRISPR-associated protein
Macromolecule | Name: TIGR03984 family CRISPR-associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 21.899844 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MPAGGRLMKN LYHYHQYEIT LESAVDSCKN HLQAAIGLLY SPQKCELVKL DNSGKLVDSY NRLKFNNLGV FEARFFNLNC ELRWVNESN GNGTAVLLSE SDITLTGFEK GLQEFITAID QQYLLWGEPA KHPPNADGWQ RLAEARIGKL DIPLDNPLKP K DRVFLTSE ...String: MPAGGRLMKN LYHYHQYEIT LESAVDSCKN HLQAAIGLLY SPQKCELVKL DNSGKLVDSY NRLKFNNLGV FEARFFNLNC ELRWVNESN GNGTAVLLSE SDITLTGFEK GLQEFITAID QQYLLWGEPA KHPPNADGWQ RLAEARIGKL DIPLDNPLKP K DRVFLTSE EYIAEVDDFG NCAVIDERLI KLEVK UniProtKB: TIGR03984 family CRISPR-associated protein |
-Macromolecule #3: Cas10
Macromolecule | Name: Cas10 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 64.335309 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAHHHHHHVG TENLYFQGFL VLIETSGNQH FIFSTNKLRE NIGASELTYL ATTEILFQGV DRVFQTNYYD QWSDTNSLNF LADSKLNPA IDDPKNNADI EILLATSGKA IALVKEEGKA KQLIKEVTKQ ALINAPGLEI GGIYVNCNWQ DKLGVAKAVK E AHKQFEVN ...String: MAHHHHHHVG TENLYFQGFL VLIETSGNQH FIFSTNKLRE NIGASELTYL ATTEILFQGV DRVFQTNYYD QWSDTNSLNF LADSKLNPA IDDPKNNADI EILLATSGKA IALVKEEGKA KQLIKEVTKQ ALINAPGLEI GGIYVNCNWQ DKLGVAKAVK E AHKQFEVN RAKRAGANGR FLRLPIAAGC SVSELPASDF DYNADGDKIP VSTVSKVKRE TAKSAKKRLR SVDGRLVNDL AQ LEKSFDE LDWLAVVHAD GNGLGQILLS LEKYIGEQTN RNYIDKYRRL SLALDNCTIN AFKMAIAVFK EDSKKIDLPI VPL ILGGDD LTVICRGDYA LEFTREFLEA FEGQTETHDD IKVIAQKAFG VDRLSACAGI SIIKPHFPFS VAYTLAERLI KSAK EVKQK VTVTNSSPIT PFPCSAIDFH ILYDSSGIDF DRIREKLRPE DNTELYNRPY VVTAAENLSQ AQGYEWSQAH SLQTL ADRV SYLRSEDGEG KSALPSSQSH ALRTALYLEK NEADAQYSLI SQRYKILKNF AEDGENKSLF HLENGKYVTR FLDALD AKD FFANANHKNQ GE UniProtKB: GGDEF domain-containing protein |
-Macromolecule #4: Cas7-2x
Macromolecule | Name: Cas7-2x / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 56.820832 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MARKVTTRWK ITGTLIAETP LHIGGVGGDA DTDLALAVNG AGEYYVPGTS LAGALRGWMT QLLNNDESQI KDLWGDHLDA KRGASFVIV DDAVIHIPNN ADVEIREGVG IDRHFGTAAN GFKYSRAVIP KGSKFKLPLT FDSQDDGLPN ALIQLLCALE A GDIRLGAA ...String: MARKVTTRWK ITGTLIAETP LHIGGVGGDA DTDLALAVNG AGEYYVPGTS LAGALRGWMT QLLNNDESQI KDLWGDHLDA KRGASFVIV DDAVIHIPNN ADVEIREGVG IDRHFGTAAN GFKYSRAVIP KGSKFKLPLT FDSQDDGLPN ALIQLLCALE A GDIRLGAA KTRGLGRIKL DDLKLKSFAL DKPEGIFSAL LDQGKKLDWN QLKANVTYQS PPYLGISITW NPKDPVMVKA EG DGLAIDI LPLVSQVGSD VRFVIPGSSI KGILRTQAER IIRTICQSNG SEKNFLEQLR INLVNELFGS ASLSQKQNGK DID LGKIGA LAVNDCFSSL SMTPDQWKAV ENATEMTGNL QPALKQATGY PNNISQAYKV LQPAMHVAVD RWTGGAAEGM LYSV LEPIG VTWEPIQVHL DIARLKNYYH GKEEKLKPAI ALLLLVLRDL ANKKIPVGYG TNRGMGTITV SQITLNGKAL PTELE PLNK TMTCPNLTDL DEAFRQDLST AWKEWIADPI DLCQQEAA UniProtKB: DUF324 domain-containing protein |
-Macromolecule #5: TIGR03986 family CRISPR-associated RAMP protein
Macromolecule | Name: TIGR03986 family CRISPR-associated RAMP protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 90.334984 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTVGTLGVVG SAKNLKLQLS FINTRQQYVQ ITLFERNSFK VAEEEFSTEL VEIIKTALPT LKNKKVEFEE DGDQIKQIRE KGQAWVGAA EQIAPYVLPS GNITETPRNV NASNFHNPYN FVPALPRDGI TGDLGDCAPA GHSYYHGDKY SGRIAVKLTT V TPLLIPDA ...String: MTVGTLGVVG SAKNLKLQLS FINTRQQYVQ ITLFERNSFK VAEEEFSTEL VEIIKTALPT LKNKKVEFEE DGDQIKQIRE KGQAWVGAA EQIAPYVLPS GNITETPRNV NASNFHNPYN FVPALPRDGI TGDLGDCAPA GHSYYHGDKY SGRIAVKLTT V TPLLIPDA SKEEINNNHK TYPVRIGKDG KPYLPPTSIK GMLRSAYEAV TNSRLAVFED HDSRLAYRMP ATMGLQMVPA RI EGDNIVL YPGTSRIGNN GRPANNDPMY AAWLPYYQNR IAYDGSRDYQ MAEHGDHVRF WAERYTRGNF CYWRVRQIAR HNQ NLGNRP ERGRNYGQHH STGVIEQFEG FVYKTNKNIG NKHDERVFII DRESIEIPLS RDLRRKWREL ITSYQEIHKK EVDR GDTGP SAVNGAVWSR QIIADESERN LSDGTLCYAH VKKEDGQYKI LNLYPVMITR GLYEIAPVDL LDETLKPATD KKQLS PADR VFGWVNQRGN GCYKGQLRIH SVTCQHDDAI DDFGNQNFSV PLAILGQPKP EQARFYCADD RKGIPLEDGY DRDDGY SDS EQGLRGRKVY PHHKGLPNGY WSNPTEDRSQ QAIQGHYQEY RRPKKDGLEQ RDDQNRSVKG WVKPLTEFTF EIDVTNL SE VELGALLWLL TLPDLHFHRL GGGKPLGFGS VRLDIDPDKT DLRNGAGWRD YYGSLLETSQ PDFTTLISQW INAFQTAV K EEYGSSSFDQ VTFIKASGQS LQGFHDNASI HYPRSTPEPK PDGEAFKWFV ANEKGRRLAL PALEKSQSFP IKPS UniProtKB: DUF324 domain-containing protein |
-Macromolecule #6: CRISPR RNA
Macromolecule | Name: CRISPR RNA / type: rna / ID: 6 / Number of copies: 1 |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 11.927167 KDa |
Sequence | String: ACUGAAACUG UAGUAGAACC AAUCGGGGUC GUCAAUA |
-Macromolecule #7: Target RNA
Macromolecule | Name: Target RNA / type: rna / ID: 7 / Number of copies: 1 |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 19.265455 KDa |
Sequence | String: CAUGACGGAU CGCGGGAGUU AUUGACGACC CCGAUUGGUU CUACUACAAA CGUGAUACUA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||
Details | Particles were monodisperse and homogeneous. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |