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Yorodumi- EMDB-40458: CryoEM structure of Deinococcus radiodurans BphP photosensory mod... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40458 | |||||||||
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Title | CryoEM structure of Deinococcus radiodurans BphP photosensory module in Pr state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phytochrome / asymmetric dimer / two component system / TRANSFERASE | |||||||||
Function / homology | Function and homology information osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans (radioresistant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Li H | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: CryoEM structure of Deinococcus radiodurans BphP photosensory module in Pr state Authors: Li H / Li H | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40458.map.gz | 167.7 MB | EMDB map data format | |
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Header (meta data) | emd-40458-v30.xml emd-40458.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40458_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_40458.png | 100.8 KB | ||
Masks | emd_40458_msk_1.map | 178 MB | Mask map | |
Filedesc metadata | emd-40458.cif.gz | 6.1 KB | ||
Others | emd_40458_half_map_1.map.gz emd_40458_half_map_2.map.gz | 165.2 MB 165.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40458 | HTTPS FTP |
-Related structure data
Related structure data | 8sgkMC 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_40458.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40458_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_40458_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40458_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Deinococcus radiodurans BphP
Entire | Name: Deinococcus radiodurans BphP |
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Components |
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-Supramolecule #1: Deinococcus radiodurans BphP
Supramolecule | Name: Deinococcus radiodurans BphP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Deinococcus radiodurans (radioresistant) |
Molecular weight | Theoretical: 163 KDa |
-Macromolecule #1: Bacteriophytochrome
Macromolecule | Name: Bacteriophytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase |
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Source (natural) | Organism: Deinococcus radiodurans (radioresistant) |
Molecular weight | Theoretical: 84.11932 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MASMTGGQQM GRGSMSRDPL PFFPPLYLGG PEITTENCER EPIHIPGSIQ PHGALLTADG HSGEVLQMSL NAATFLGQEP TVLRGQTLA ALLPEQWPAL QAALPPGCPD ALQYRATLDW PAAGHLSLTV HRVGELLILE FEPTEAWDST GPHALRNAMF A LESAPNLR ...String: MASMTGGQQM GRGSMSRDPL PFFPPLYLGG PEITTENCER EPIHIPGSIQ PHGALLTADG HSGEVLQMSL NAATFLGQEP TVLRGQTLA ALLPEQWPAL QAALPPGCPD ALQYRATLDW PAAGHLSLTV HRVGELLILE FEPTEAWDST GPHALRNAMF A LESAPNLR ALAEVATQTV RELTGFDRVM LYKFAPDATG EVIAEARREG LHAFLGHRFP ASDIPAQARA LYTRHLLRLT AD TRAAAVP LDPVLNPQTN APTPLGGAVL RATSPMHMQY LRNMGVGSSL SVSVVVGGQL WGLIACHHQT PYVLPPDLRT TLE YLGRLL SLQVQVKEAA DVAAFRQSLR EHHARVALAA AHSLSPHDTL SDPALDLLGL MRAGGLILRF EGRWQTLGEV PPAP AVDAL LAWLETQPGA LVQTDALGQL WPAGADLAPS AAGLLAISVG EGWSECLVWL RPELRLEVAW GGATPDQAKD DLGPR HSFD TYLEEKRGYA EPWHPGEIEE AQDLRDTLTG ALGERLSVIR DLNRALTQSN AEWRQYGFVI SHHMQEPVRL ISQFAE LLT RQPRAQDGSP DSPQTERITG FLLRETSRLR SLTQDLHTYT ALLSAPPPVR RPTPLGRVVD DVLQDLEPRI ADTGASI EV APELPVIAAD AGLLRDLLLH LIGNALTFGG PEPRIAVRTE RQGAGWSIAV SDQGAGIAPE YQERIFLLFQ RLGSLDEA L GNGLGLPLCR KIAELHGGTL TVESAPGEGS TFRCWLPDAG PLPGAADALE HHHHHH UniProtKB: Bacteriophytochrome |
-Macromolecule #2: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidan...
Macromolecule | Name: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene- ...Name: 3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid type: ligand / ID: 2 / Number of copies: 2 / Formula: LBV |
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Molecular weight | Theoretical: 585.67 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL | |||||||||
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Buffer | pH: 6.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY | |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 193.0 K / Max: 193.0 K |
Alignment procedure | Coma free - Residual tilt: 0.05 mrad |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 8447 / Average exposure time: 1.0 sec. / Average electron dose: 66.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8sgk: |