+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15685 | |||||||||
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Title | Cryo-EM structure of DrBphP in Pr state | |||||||||
Map data | ||||||||||
Sample |
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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 / phosphorelay sensor kinase activity / photoreceptor activity / phosphorelay signal transduction system / regulation of DNA-templated transcription / ATP binding / identical protein binding Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans R1 (radioresistant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||
Authors | Wahlgren WY / Takala H / Westenhoff S | |||||||||
Funding support | European Union, Finland, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural mechanism of signal transduction in a phytochrome histidine kinase Authors: Wahlgren WY / Claesson E / Tuure I / Trillo-Muyo S / Bodizs S / Ihalainen JA / Takala H / Westenhoff S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15685.map.gz | 263.7 MB | EMDB map data format | |
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Header (meta data) | emd-15685-v30.xml emd-15685.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15685_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_15685.png | 57.9 KB | ||
Masks | emd_15685_msk_1.map | 343 MB | Mask map | |
Others | emd_15685_half_map_1.map.gz emd_15685_half_map_2.map.gz | 258.6 MB 258.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15685 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15685 | HTTPS FTP |
-Related structure data
Related structure data | 8avwM 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_15685.map.gz / Format: CCP4 / Size: 343 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: 0.8617 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15685_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15685_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15685_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Full-length bacteriophytochrome fused to its response regulator f...
Entire | Name: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans. |
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Components |
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-Supramolecule #1: Full-length bacteriophytochrome fused to its response regulator f...
Supramolecule | Name: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans. type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Deinococcus radiodurans R1 (radioresistant) |
Molecular weight | Theoretical: 101 KDa |
-Macromolecule #1: Bacteriophytochrome,Response regulator
Macromolecule | Name: Bacteriophytochrome,Response regulator / type: protein_or_peptide / ID: 1 Details: Sample is a fusion of Deinococcus radiodurans DrBphP and its response regulator DrRR.,Sample is a fusion of Deinococcus radiodurans DrBphP and its response regulator DrRR. Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase |
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Source (natural) | Organism: Deinococcus radiodurans R1 (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 |
Molecular weight | Theoretical: 101.579164 KDa |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
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 PLPGAADAAS SAGGSAGSAG MPERASVPLR LLLVEDNAA DIFLMEMALE YSSVHTELLV ARDGLEALEL LEQAKTGGPF PDLILLDLNM PRVDGFELLQ ALRADPHLAH LPAIVLTTSN DPSDVKRAY ALQANSYLTK PSTLEDFLQL IERLTAYWFG TAAIPQTYQP QLEHHHHHH |
-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
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.3 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |