+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43754 | |||||||||
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Title | BsaXI-DNA complex I | |||||||||
Map data | BsaXI-DNA complex (P40-J522) conformation I map file P40-J538 | |||||||||
Sample |
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Keywords | restriction nuclease / restriction-modification systems / Type IIB / R-M complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | |||||||||
Function / homology | Function and homology information N-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding Similarity search - Function | |||||||||
Biological species | Geobacillus stearothermophilus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||
Authors | Shen BW / Stoddard BL / Xu S | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structural and biochemical analysis of subunit assembly, DNA recognition and cleavage by a Type IIB restriction-modification enzyme: BsaXI Authors: Shen BW / Heiter D / Xu S / Stoddard BL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43754.map.gz | 69 MB | EMDB map data format | |
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Header (meta data) | emd-43754-v30.xml emd-43754.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43754_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_43754.png | 119.4 KB | ||
Masks | emd_43754_msk_1.map | 137.1 MB | Mask map | |
Filedesc metadata | emd-43754.cif.gz | 8 KB | ||
Others | emd_43754_half_map_1.map.gz emd_43754_half_map_2.map.gz | 127.4 MB 127.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43754 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43754 | HTTPS FTP |
-Validation report
Summary document | emd_43754_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_43754_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_43754_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_43754_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43754 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43754 | HTTPS FTP |
-Related structure data
Related structure data | 8w2pMC 8w2qC 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_43754.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | BsaXI-DNA complex (P40-J522) conformation I map file P40-J538 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.12 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_43754_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: BsaXI-DNA J522 half map P40-J538-A
File | emd_43754_half_map_1.map | ||||||||||||
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Annotation | BsaXI-DNA J522 half map P40-J538-A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: BsaXI-DNA complex conformation I (J538) P40-J538-half-map-B
File | emd_43754_half_map_2.map | ||||||||||||
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Annotation | BsaXI-DNA complex conformation I (J538) P40-J538-half-map-B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Quaternary complex of RM, S and DNA complex
Entire | Name: Quaternary complex of RM, S and DNA complex |
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Components |
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-Supramolecule #1: Quaternary complex of RM, S and DNA complex
Supramolecule | Name: Quaternary complex of RM, S and DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230 |
Molecular weight | Theoretical: 2.69 kDa/nm |
-Macromolecule #1: site-specific DNA-methyltransferase (adenine-specific)
Macromolecule | Name: site-specific DNA-methyltransferase (adenine-specific) type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO EC number: site-specific DNA-methyltransferase (adenine-specific) |
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Source (natural) | Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230 |
Molecular weight | Theoretical: 107.195234 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKNWQRIVEA KLEQQKHKVA EISLENGTVN YSKKIKHNRN LKALTGDEEI VRAFLIDRLV NELDYKPEYL ETEKEYTIKG GHSKINPRV DVLVKDDKGN PFFFIEVKAP NKFEEDKDEI EGQLFALAQA EERDFKTKVK YLVYYTVELI DDEIVDRAII I DFEKYPTY ...String: MKNWQRIVEA KLEQQKHKVA EISLENGTVN YSKKIKHNRN LKALTGDEEI VRAFLIDRLV NELDYKPEYL ETEKEYTIKG GHSKINPRV DVLVKDDKGN PFFFIEVKAP NKFEEDKDEI EGQLFALAQA EERDFKTKVK YLVYYTVELI DDEIVDRAII I DFEKYPTY TDWSNGGFIS TGTELTAGYG EPKKQPLIKG HEKYDLRVRI DREEIEGLGR NLHNVLWGGG GTNDSEIFYS LV NIILAKI QDEYEKEDGQ EYDFQVYQYG DNVESPQKLF DRINALYKRA LREQLNVTDE QKIAEDNVIN RNKFPLNKLV YTV QALESL SFLEGRNSLD GKDILGDFFE SIIRDGFKQT KGQFFTPTPI VKFILYALQL DKLAIDRLNN DRELPLIIDP SAGS GTFLI EAMKLITKEV KYKQNHKVKS SRQITKRFEE LFMPDHNENK WAREYLYGCE INFDLGTASK VNMILHGDGS ANIFV QDGL LPFRFYVKET SPNYLETASP DALYGDKEVN GKFDVVVSNP PFSVDLDTQT QREVRNAFLF GDKKNSENLF IERYYQ LLK EGGRLGVVLP ESVFDTTENK YIRLFIFKYF KVKAVVSLPQ VTFEPFTSTK TSLLFAQKKT KEEVEQWNEL WDKYGKE WS LLKTRINDYF SYFVKGRPLN KKWAPDVVKD IQEGNEDNIR KNIFRFLKDH IKEEDKNLEI KDLLIKYAEE ISSISKHE K ETDVFGFYNA WWVFGEVAKE LDYPIFMAEA ENVGYKRTKK GEKPMPNDLY DLEYAPSTLD CEKVLSSFDI EINALEASK TKLSVEKGLL EEKLKDKEDK ENEKIQKRLN KISELLETIE NQLDSIRSKK LEVEGILEKY YENNKLKEEY SERDDEELIN HFKHGVLYQ YRSEDILLRN KTVHKILDEI RQGVIWD UniProtKB: Site-specific DNA-methyltransferase (adenine-specific) |
-Macromolecule #2: S.BsaXI
Macromolecule | Name: S.BsaXI / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Geobacillus stearothermophilus (bacteria) / Strain: Cpw230 |
Molecular weight | Theoretical: 55.038824 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGLIQRRNFS TFASEPSVRF DFNYMKSVTP TTEEYYTYKS LFEVVPSTVP TLDESEPFKY AEIGHVSKNG EVFPVTLSFE DRDELNEDL FKKIEKGDIF LPERGNILIS AIRPYLNKIV LIKEDDKTDI YFTKAFIQIK PLINSRILYY ALRTIFSEKI N AVSRQGKG ...String: MGLIQRRNFS TFASEPSVRF DFNYMKSVTP TTEEYYTYKS LFEVVPSTVP TLDESEPFKY AEIGHVSKNG EVFPVTLSFE DRDELNEDL FKKIEKGDIF LPERGNILIS AIRPYLNKIV LIKEDDKTDI YFTKAFIQIK PLINSRILYY ALRTIFSEKI N AVSRQGKG YPTLKEDDLK TIQFSKKVID NLLAKEEELI SNIDALEKDI KELKSIQRSK KEIVDEVFSS HFNINMVELM AL DSQRRVD VGLSSISSLN STIRYSYRWN KMKLIQKYLY RDIDCIEPLG KYILSSNNGW SPESVVGGEG IPILGQEHLE FDG VLNVSP TKATTKTKNN MENFFIQEGD LFISRGNTVD LVGLACVVET EVTEDIIYPD LYIRLKIDEK VIHKKYLALL FNSF FGRLY FKYVSKGKNQ TMVKISSNEL LNYYLPIPPM EEQLEIVGKI EEQIGAQNEI EKQIEEKRNQ IRVIIEETAR S UniProtKB: Uncharacterized protein |
-Macromolecule #3: DNA (41-MER) Top strand of BsaXI cognate DNA substrate
Macromolecule | Name: DNA (41-MER) Top strand of BsaXI cognate DNA substrate type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Geobacillus stearothermophilus (bacteria) |
Molecular weight | Theoretical: 16.083387 KDa |
Sequence | String: (DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DT)(DT)(DG)(DT)(DC)(DG)(DG) (DA)(DA)(DC)(DC)(DA)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG)(DA) (DA) (DT)(DT)(DA)(DA)(DT)(DA) ...String: (DA)(DA)(DT)(DA)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DT)(DA)(DT)(DT)(DG)(DT)(DC)(DG)(DG) (DA)(DA)(DC)(DC)(DA)(DA)(DG)(DT)(DC) (DT)(DC)(DC)(DA)(DT)(DA)(DT)(DG)(DG)(DA) (DA) (DT)(DT)(DA)(DA)(DT)(DA)(DA)(DG) (DC)(DT)(DA)(DG) |
-Macromolecule #4: DNA (41-MER) Complementary strand of BsaXI DNA substrate
Macromolecule | Name: DNA (41-MER) Complementary strand of BsaXI DNA substrate type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Geobacillus stearothermophilus (bacteria) |
Molecular weight | Theoretical: 15.963281 KDa |
Sequence | String: (DC)(DT)(DA)(DG)(DC)(DT)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DC)(DC)(DA)(DT)(DA)(DT) (DG)(DG)(6MA)(DG)(DA)(DC)(DT)(DT)(DG) (DG)(DT)(DT)(DC)(DC)(DG)(DA)(DC)(DA)(DA) (DT)(DA)(DT)(DT)(DC)(DA)(DG) ...String: (DC)(DT)(DA)(DG)(DC)(DT)(DT)(DA)(DT)(DT) (DA)(DA)(DT)(DT)(DC)(DC)(DA)(DT)(DA)(DT) (DG)(DG)(6MA)(DG)(DA)(DC)(DT)(DT)(DG) (DG)(DT)(DT)(DC)(DC)(DG)(DA)(DC)(DA)(DA) (DT)(DA)(DT)(DT)(DC)(DA)(DG)(DC)(DT) (DT)(DA)(DT)(DT) |
-Macromolecule #5: S-ADENOSYLMETHIONINE
Macromolecule | Name: S-ADENOSYLMETHIONINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SAM |
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Molecular weight | Theoretical: 398.437 Da |
Chemical component information | ChemComp-SAM: |
-Macromolecule #6: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #7: S-ADENOSYL-L-HOMOCYSTEINE
Macromolecule | Name: S-ADENOSYL-L-HOMOCYSTEINE / type: ligand / ID: 7 / Number of copies: 1 / Formula: SAH |
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Molecular weight | Theoretical: 384.411 Da |
Chemical component information | ChemComp-SAH: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 5 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-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: 8 / Component - Concentration: 20.0 mM / Component - Name: TrisHCl / Details: 20 mM TrisHCl, 250 mM Nacl, 2 mM CaCl2 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
Details | Sample was monodisperse. |
-Electron microscopy #1
Microscopy ID | 1 |
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Microscope | FEI TALOS ARCTICA |
Temperature | Min: 170.0 K |
Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Image recording ID: 1 / Film or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 2-50 / Number grids imaged: 3 / Number real images: 1579 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 5.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Electron microscopy #1~
Microscopy ID | 1 |
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Microscope | FEI TITAN KRIOS |
Temperature | Min: 170.0 K / Max: 170.0 K |
Specialist optics | Phase plate: OTHER |
Image recording | Image recording ID: 2 / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: COUNTING / Digitization - Frames/image: 2-50 / Number grids imaged: 1 / Number real images: 2238 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 3000 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: Other / Chain - Initial model type: experimental model / Details: manual built model in coot |
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Refinement | Space: REAL / Protocol: BACKBONE TRACE |
Output model | PDB-8w2p: |