+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36947 | |||||||||
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Title | Structure of procaryotic Ago | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ago / DNA/RNA / DNA BINDING PROTEIN / CELL INVASION / DNA-RNA-CELL INVASION complex | |||||||||
Function / homology | SIR2-like domain / SIR2-like domain / DHS-like NAD/FAD-binding domain superfamily / nucleic acid binding / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Piwi domain protein / Sir2 superfamily protein Function and homology information | |||||||||
Biological species | Geobacter sulfurreducens (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Gao X / Sun D / Cui S / Wang Y | |||||||||
Funding support | 1 items
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Citation | Journal: To Be Published Title: Structural Basis of prokaryotic Argonaute System Authors: Gao X / Cui S / Sun D / Wang Y | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36947.map.gz | 84 MB | EMDB map data format | |
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Header (meta data) | emd-36947-v30.xml emd-36947.xml | 17.5 KB 17.5 KB | Display Display | EMDB header |
Images | emd_36947.png | 49.9 KB | ||
Masks | emd_36947_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-36947.cif.gz | 6.5 KB | ||
Others | emd_36947_half_map_1.map.gz emd_36947_half_map_2.map.gz | 95.8 MB 95.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36947 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36947 | HTTPS FTP |
-Validation report
Summary document | emd_36947_validation.pdf.gz | 860.4 KB | Display | EMDB validaton report |
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Full document | emd_36947_full_validation.pdf.gz | 860 KB | Display | |
Data in XML | emd_36947_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_36947_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36947 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36947 | HTTPS FTP |
-Related structure data
Related structure data | 8k88MC 8k87C 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_36947.map.gz / Format: CCP4 / Size: 103 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: 0.5044 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_36947_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map generated from cryosparc
File | emd_36947_half_map_1.map | ||||||||||||
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Annotation | half map generated from cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map generated from cryosparc
File | emd_36947_half_map_2.map | ||||||||||||
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Annotation | half map generated from cryosparc | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Short Prokaryotic Argonaute associated Sir2
Entire | Name: Short Prokaryotic Argonaute associated Sir2 |
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Components |
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-Supramolecule #1: Short Prokaryotic Argonaute associated Sir2
Supramolecule | Name: Short Prokaryotic Argonaute associated Sir2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Molecular weight | Theoretical: 120 kDa/nm |
-Macromolecule #1: DNA (41-mer)
Macromolecule | Name: DNA (41-mer) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 12.525115 KDa |
Sequence | String: (DC)(DG)(DA)(DA)(DA)(DC)(DA)(DA)(DC)(DA) (DC)(DA)(DG)(DC)(DT)(DC)(DT)(DA)(DA)(DC) (DC)(DG)(DA)(DC)(DG)(DT)(DC)(DT)(DA) (DA)(DG)(DA)(DA)(DA)(DC)(DC)(DA)(DT)(DT) (DA) (DT) |
-Macromolecule #2: DNA/RNA (21-mer)
Macromolecule | Name: DNA/RNA (21-mer) / type: other / ID: 2 / Number of copies: 1 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 6.675973 KDa |
Sequence | String: AUAAUGGUUU CUUAGACGUC (DG) |
-Macromolecule #3: Piwi domain protein
Macromolecule | Name: Piwi domain protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Molecular weight | Theoretical: 53.325566 KDa |
Recombinant expression | Organism: Expression vector pET-mod (others) |
Sequence | String: MADNLSQLAA HSTIPEPLLL FKDNRTDTHP LRGLSQYGPY SACFNLPGQV RLAYLAPTEH MRKLDAIVRE LQNPATPKEA TNYYVEYGG FEKVFKVPLV MPQEHLRCLA LDECHGVAAN GNGLALADKI VQSMSGLFRQ KHAFDVLLVY LPASWKKCFE Y DGFDLHDR ...String: MADNLSQLAA HSTIPEPLLL FKDNRTDTHP LRGLSQYGPY SACFNLPGQV RLAYLAPTEH MRKLDAIVRE LQNPATPKEA TNYYVEYGG FEKVFKVPLV MPQEHLRCLA LDECHGVAAN GNGLALADKI VQSMSGLFRQ KHAFDVLLVY LPASWKKCFE Y DGFDLHDR IKAKVAPLNL PIQIINDTAL TRQCRANVMW GVSVALYAKA GGIPWKLADW DKDEAYIGLS YAIKKNAEGQ EY TTCCSQV FDPDGTGFEF VAYDTREFIT DRKGNPYLSY QEMQSVLSKS LHLYQSSHNG RMPRKIFIHK TTHFTEDEIQ GAF DSFSSS TEIELVQIIQ STNWYGLKVD GKKGDKPVAP ASYPVDRGLY QPLTESECLL WTQGSVMGVN QQNPGQPVFK EAAL TPLPN PIMLRRFSGN GGWHATCSSI LALTKVDWNN NTLYKKLPVT LVYSQVFADV VKQTPEIVNE IYDYRFFM UniProtKB: Piwi domain protein |
-Macromolecule #4: Sir2 superfamily protein
Macromolecule | Name: Sir2 superfamily protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Geobacter sulfurreducens (bacteria) |
Molecular weight | Theoretical: 66.645922 KDa |
Recombinant expression | Organism: Expression vector pET-mod (others) |
Sequence | String: MDVLTDNEFY QHYLQNSQHM MWFLGAGTSR SAGLPTASDI IWDLKHRYYC LHENQDYQKH DINNHAIKSK IQSYMDSKGF PLQWSPEEY SFYFELVFRD DYEAQRKYLL EALASRKVSL NIGHRVLAAL LEMNQTKVVF TTNFDDVIET AFSDISGKHL S VYHLEGSY ...String: MDVLTDNEFY QHYLQNSQHM MWFLGAGTSR SAGLPTASDI IWDLKHRYYC LHENQDYQKH DINNHAIKSK IQSYMDSKGF PLQWSPEEY SFYFELVFRD DYEAQRKYLL EALASRKVSL NIGHRVLAAL LEMNQTKVVF TTNFDDVIET AFSDISGKHL S VYHLEGSY AALSALNTEA FPIYAKIHGD FRYQKIKNLT PDLQTNDREI HKCFLAAAIR FGLVVSGYSG RDENVMTMLR AA IDQNNAF PHGLYWTVPS ISKSEPAVQD LITYAQGKGV RAYLVETGTF DEMLSKIWRQ VKDKPAAIDA KVRTARVCPV SIP LPGPGK SFPALRTNAL PVVTQSIRCG VVTLASPITF SELKERISQK SPKALLTYTE KVLFLGGEPE IRKIFSNDEI NSIG QYYID EIAQSVAAST FLKSFVEEAI LTALLREKPI LHRVRHRTHY AVIPNASAKD DRFLDLRKAV GFKGDLGYIT GNVTN AKEL SWAEAVSIRL EERGGKLWIM LKPEIWIKPL DRREEATDFI RSRRRYRFNQ CSYQILDAWI KILFGSIGGG GTVNIS CFP DAEFKAEFEI GTRTAFSLGV GYGR UniProtKB: Sir2 superfamily protein |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Grid | Material: NICKEL/TITANIUM / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: cryosaprc Ab-initio Reconstruction |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1431771 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |