+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36047 | |||||||||
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Title | Structure of the SPARTA complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | complex / immune / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA-DNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Maribacter polysiphoniae (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Guo M / Zhu Y / Lin Z / Huang Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2023 Title: Cryo-EM structure of the ssDNA-activated SPARTA complex. Authors: Minghui Guo / Yuwei Zhu / Zhiying Lin / Dehui Yang / Anqi Zhang / Changyou Guo / Zhiwei Huang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36047.map.gz | 123 MB | EMDB map data format | |
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Header (meta data) | emd-36047-v30.xml emd-36047.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_36047.png | 107.7 KB | ||
Filedesc metadata | emd-36047.cif.gz | 6.2 KB | ||
Others | emd_36047_half_map_1.map.gz emd_36047_half_map_2.map.gz | 226.9 MB 226.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36047 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36047 | HTTPS FTP |
-Validation report
Summary document | emd_36047_validation.pdf.gz | 740.5 KB | Display | EMDB validaton report |
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Full document | emd_36047_full_validation.pdf.gz | 740.1 KB | Display | |
Data in XML | emd_36047_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | emd_36047_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36047 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36047 | HTTPS FTP |
-Related structure data
Related structure data | 8j7sMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36047.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.0773 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36047_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36047_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : SPARTA complex
Entire | Name: SPARTA complex |
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Components |
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-Supramolecule #1: SPARTA complex
Supramolecule | Name: SPARTA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
-Macromolecule #1: Piwi domain-containing protein
Macromolecule | Name: Piwi domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
Molecular weight | Theoretical: 57.978254 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKELIYIEEP KILFAHGQKC TDARDGLALF GPLNNLYGIK SGVIGTKQGL KIFRDYLDHI QKPIYNSNSI TRPMFPGFEA VFDCKWEST GITFKEVTNE DIGKFLYNSS THKRTYDLVS LFIDKIISAN KNEDENVDVW FVIVPDEIYK YCRPNSVLPK E MVQTKALM ...String: MKELIYIEEP KILFAHGQKC TDARDGLALF GPLNNLYGIK SGVIGTKQGL KIFRDYLDHI QKPIYNSNSI TRPMFPGFEA VFDCKWEST GITFKEVTNE DIGKFLYNSS THKRTYDLVS LFIDKIISAN KNEDENVDVW FVIVPDEIYK YCRPNSVLPK E MVQTKALM SKSKAKSFRY EPSLFPDINI ELKEQEKEAE TYNYDAQFHD QFKARLLKHT IPTQIFREST LAWRDFKNAF GL PIRDFSK IEGHLAWTIS TAAFYKAGGK PWKLSDVRNG VCYLGLVYKK VEKSKNPRNA CCAAQMFLDN GDGTVFKGEV GPW YNPKNG QYHLEPKEAK ALLSQSLQSY KEQIGEYPKE VFIHAKTRFN HQEWDAFLEV TPKETNLVGV TISKTKPLKL YKTE GDYTI LRGNAYVVNE RSAFLWTVGY VPKIQTALSM EVPNPLFIEI NKGEADIKQV LKDILSLTKL NYNACIFADG EPVTL RFAD KIGEILTAST DIKTPPLAFK YY UniProtKB: Piwi domain-containing protein |
-Macromolecule #2: TIR domain-containing protein
Macromolecule | Name: TIR domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
Molecular weight | Theoretical: 49.39659 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MRNKIFISHA TPDDNDFTRW LALKLIGLGY EVWCDILFLD KGVDFWSNIE KVIREDTCKF LLVSSSYSNQ REGVLKELAV AAKVKKQLK DDKFIIPLAI DEQLSYDDIN IDIVRLNAID FKMSWARGLK DILEAFEKQK VPKEVADASK SNLLYQQIFL H DKSVIEKE ...String: MRNKIFISHA TPDDNDFTRW LALKLIGLGY EVWCDILFLD KGVDFWSNIE KVIREDTCKF LLVSSSYSNQ REGVLKELAV AAKVKKQLK DDKFIIPLAI DEQLSYDDIN IDIVRLNAID FKMSWARGLK DILEAFEKQK VPKEVADASK SNLLYQQIFL H DKSVIEKE EIYDSNWLSI LSFPEELRFH EYNWMLPKRF DVRELTFPAV RYKNYLCTFA WAYDFTYHLP KTETYHKSKT IR IPTEEIL SGSYDSNFIR NAECKRLIVQ LLNKAFELRM KDKEVQEYEM SNKTAYWLEK GKLEKDKFEK TMLVGKQKDK NWH FAISGA SKLYPFPVLM ISSHIFFTAD GKKLIDSSSV QHSSRRRQGK NWWNNTWRTK LLAFIKYLSD DDTSFYLEMG SEEK VFVSN EPVKFKGNVS YNI UniProtKB: TIR domain-containing protein |
-Macromolecule #3: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP...
Macromolecule | Name: RNA (5'-R(P*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*A)-3') type: rna / ID: 3 / Number of copies: 4 |
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Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
Molecular weight | Theoretical: 6.000577 KDa |
Sequence | String: UGACGGCUCU AAUCUAUUA |
-Macromolecule #4: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP...
Macromolecule | Name: DNA (5'-D(P*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*CP*AP*AP*TP*AP*GP*A)-3') type: dna / ID: 4 / Number of copies: 4 / Classification: DNA |
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Source (natural) | Organism: Maribacter polysiphoniae (bacteria) |
Molecular weight | Theoretical: 7.425842 KDa |
Sequence | String: (DT)(DA)(DA)(DT)(DA)(DG)(DA)(DT)(DT)(DA) (DG)(DA)(DG)(DC)(DC)(DG)(DT)(DC)(DA)(DA) (DT)(DA)(DG)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: NITROGEN |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 832006 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |