+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36621 | |||||||||
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Title | Cryo-EM structure of a DNA-protein complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA / protein / interaction / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermococcus thioreducens (archaea) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Li Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of a DNA-protein complex Authors: Li Z | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36621.map.gz | 49.6 MB | EMDB map data format | |
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Header (meta data) | emd-36621-v30.xml emd-36621.xml | 14.9 KB 14.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36621_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_36621.png | 95.6 KB | ||
Filedesc metadata | emd-36621.cif.gz | 5.8 KB | ||
Others | emd_36621_half_map_1.map.gz emd_36621_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36621 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36621 | HTTPS FTP |
-Validation report
Summary document | emd_36621_validation.pdf.gz | 945.7 KB | Display | EMDB validaton report |
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Full document | emd_36621_full_validation.pdf.gz | 945.3 KB | Display | |
Data in XML | emd_36621_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | emd_36621_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36621 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36621 | HTTPS FTP |
-Related structure data
Related structure data | 8jsiMC 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_36621.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_36621_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36621_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : a DNA-protein complex
Entire | Name: a DNA-protein complex |
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Components |
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-Supramolecule #1: a DNA-protein complex
Supramolecule | Name: a DNA-protein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Thermococcus thioreducens (archaea) |
-Macromolecule #1: Argonaute family protein
Macromolecule | Name: Argonaute family protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Thermococcus thioreducens (archaea) |
Molecular weight | Theoretical: 87.488398 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MLMKVLTNMV KLNQDIIPNE IYLYKIFNKP EDGMNIYKIA YRNHGIVIDP QNRIIATPSE LEYSGKFAIE DEISFNELPE NYQNRLVLR ILRDNGISDH ALSRTLQKYR KPKPFGDFEV IPEIRSSVIK HGGDFYLVLH LSHQIRSKKT LWELVGRNKD A LRDFLKEH ...String: MLMKVLTNMV KLNQDIIPNE IYLYKIFNKP EDGMNIYKIA YRNHGIVIDP QNRIIATPSE LEYSGKFAIE DEISFNELPE NYQNRLVLR ILRDNGISDH ALSRTLQKYR KPKPFGDFEV IPEIRSSVIK HGGDFYLVLH LSHQIRSKKT LWELVGRNKD A LRDFLKEH RGTILLRDIA SEHKVVYKPI FKRYNGDPDL IEDNSNDVEH WYDYHLERYW NTPELKKEFY KKFGPVDLNQ PI ILAKPLR QHNRGDLVHL LPQFVVPVYN AEQLNDILAS EILEYLKLTS NQRISLLSRL INDIKTNTNI IVSSLTELEA NTF DVDLND MLQVRNADNV KVTLSELEIS KTRLFTWMKS RKYPVILPYD IPQKLKKIEK IPVFIIVDSA LSRDIQTFAK DEFR YLISS LQKSLSNWVD FPILDIRDKY IFTIDLTSDK DIVNLSIKLV NLMKNAELGL ALIATRTKLP NETFDEVKKR LFSVN IISQ VVNEATLYKR DKYNESRLNL YVQHNLLFQI LSKLGIKYYV LRHKFSYDYI VGIDVTPMKL SHGYIGGSAV MFDSQG YIR KIIPVEIGEQ MGESIDMKEF FKDMVVQFGK FGIDLEGKSI LILRDGKITK DEEEGLAYIS KVFGIKITTF NIVKRHL LR IFANRKLYLR LANSVYLLPH RIKQSVGTPV PLKLSEKRLI LDGTITSQEI TYNDIFEILL LSELNYGSIS ADMKLPAP V HYAHKFVRAL RKGWRIREEL LAEGFLYFV UniProtKB: Argonaute family protein |
-Macromolecule #2: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*C)-3')
Macromolecule | Name: DNA (5'-D(P*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*CP*C)-3') type: dna / ID: 2 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Thermococcus thioreducens (archaea) |
Molecular weight | Theoretical: 4.747109 KDa |
Sequence | String: (DA)(DC)(DA)(DA)(DC)(DC)(DT)(DA)(DC)(DT) (DA)(DC)(DC)(DT)(DC)(DC) |
-Macromolecule #3: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3')
Macromolecule | Name: DNA (5'-D(P*GP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*T)-3') type: dna / ID: 3 / Number of copies: 2 / Classification: DNA |
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Source (natural) | Organism: Thermococcus thioreducens (archaea) |
Molecular weight | Theoretical: 5.049273 KDa |
Sequence | String: (DG)(DG)(DA)(DG)(DG)(DT)(DA)(DG)(DT)(DA) (DG)(DG)(DT)(DT)(DG)(DT) |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 6 / 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
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: 54.0 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: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |