+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35415 | |||||||||
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Title | Cryo-EM structure of Arabidopsis phytochrome A. | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phytochrome / Pr state / GENE REGULATION | |||||||||
Function / homology | Function and homology information response to continuous far red light stimulus by the high-irradiance response system / response to very low fluence red light stimulus / far-red light photoreceptor activity / red light signaling pathway / red or far-red light photoreceptor activity / gravitropism / response to far red light / phototropism / photomorphogenesis / detection of visible light ...response to continuous far red light stimulus by the high-irradiance response system / response to very low fluence red light stimulus / far-red light photoreceptor activity / red light signaling pathway / red or far-red light photoreceptor activity / gravitropism / response to far red light / phototropism / photomorphogenesis / detection of visible light / response to arsenic-containing substance / phosphorelay sensor kinase activity / response to cold / nuclear body / negative regulation of translation / protein kinase activity / nuclear speck / mRNA binding / regulation of DNA-templated transcription / protein homodimerization activity / identical protein binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Ma L / Zhou C / Wang J / Guan Z / Yin P | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2023 Title: Plant phytochrome A in the Pr state assembles as an asymmetric dimer. Authors: Jiao Wang / Chen Zhou / Zeyuan Guan / Qiang Wang / Jun Zhao / Lixia Wang / Liuqing Zhang / Delin Zhang / Xing Wang Deng / Ling Ma / Ping Yin / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35415.map.gz | 78.8 MB | EMDB map data format | |
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Header (meta data) | emd-35415-v30.xml emd-35415.xml | 17 KB 17 KB | Display Display | EMDB header |
Images | emd_35415.png | 59.5 KB | ||
Filedesc metadata | emd-35415.cif.gz | 6.1 KB | ||
Others | emd_35415_additional_1.map.gz emd_35415_half_map_1.map.gz emd_35415_half_map_2.map.gz | 77.4 MB 77.7 MB 77.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35415 | HTTPS FTP |
-Validation report
Summary document | emd_35415_validation.pdf.gz | 791.9 KB | Display | EMDB validaton report |
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Full document | emd_35415_full_validation.pdf.gz | 791.5 KB | Display | |
Data in XML | emd_35415_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | emd_35415_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35415 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35415 | HTTPS FTP |
-Related structure data
Related structure data | 8iffMC 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_35415.map.gz / Format: CCP4 / Size: 83.7 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
-Additional map: This map was 3.4 angstrom with improved HKRD domain
File | emd_35415_additional_1.map | ||||||||||||
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Annotation | This map was 3.4 angstrom with improved HKRD domain | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35415_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35415_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Phytochrome A
Entire | Name: Phytochrome A |
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Components |
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-Supramolecule #1: Phytochrome A
Supramolecule | Name: Phytochrome A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
-Macromolecule #1: Phytochrome A
Macromolecule | Name: Phytochrome A / type: protein_or_peptide / ID: 1 Details: Author stated the additional map was 3.4 angstrom with improved HKRD domain. Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 124.652773 KDa |
Recombinant expression | Organism: Arabidopsis (plant) |
Sequence | String: MSGSRPTQSS EGSRRSRHSA RIIAQTTVDA KLHADFEESG SSFDYSTSVR VTGPVVENQP PRSDKVTTTY LHHIQKGKLI QPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH C RTSAKPFY ...String: MSGSRPTQSS EGSRRSRHSA RIIAQTTVDA KLHADFEESG SSFDYSTSVR VTGPVVENQP PRSDKVTTTY LHHIQKGKLI QPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH C RTSAKPFY AIIHRVTGSI IIDFEPVKPY EVPMTAAGAL QSYKLAAKAI TRLQSLPSGS MERLCDTMVQ EVFELTGYDR VM AYKFHED DHGEVVSEVT KPGLEPYLGL HYPATDIPQA ARFLFMKNKV RMIVDCNAKH ARVLQDEKLS FDLTLCGSTL RAP HSCHLQ YMANMDSIAS LVMAVVVNEE DGEGDAPDAT TQPQKRKRLW GLVVCHNTTP RFVPFPLRYA CEFLAQVFAI HVNK EVELD NQMVEKNILR TQTLLCDMLM RDAPLGIVSQ SPNIMDLVKC DGAALLYKDK IWKLGTTPSE FHLQEIASWL CEYHM DSTG LSTDSLHDAG FPRALSLGDS VCGMAAVRIS SKDMIFWFRS HTAGEVRWGG AKHDPDDRDD ARRMHPRSSF KAFLEV VKT RSLPWKDYEM DAIHSLQLIL RNAFKDSETT DVNTKVIYSK LNDLKIDGIQ ELEAVTSEMV RLIETATVPI LAVDSDG LV NGWNTKIAEL TGLSVDEAIG KHFLTLVEDS SVEIVKRMLE NALEGTEEQN VQFEIKTHLS RADAGPISLV VNACASRD L HENVVGVCFV AHDLTGQKTV MDKFTRIEGD YKAIIQNPNP LIPPIFGTDE FGWCTEWNPA MSKLTGLKRE EVIDKMLLG EVFGTQKSCC RLKNQEAFVN LGIVLNNAVT SQDPEKVSFA FFTRGGKYVE CLLCVSKKLD REGVVTGVFC FLQLASHELQ QALHVQRLA ERTAVKRLKA LAYIKRQIRN PLSGIMFTRK MIEGTELGPE QRRILQTSAL CQKQLSKILD DSDLESIIEG C LDLEMKEF TLNEVLTAST SQVMMKSNGK SVRITNETGE EVMSDTLYGD SIRLQQVLAD FMLMAVNFTP SGGQLTVSAS LR KDQLGRS VHLANLEIRL THTGAGIPEF LLNQMFGTEE DVSEEGLSLM VSRKLVKLMN GDVQYLRQAG KSSFIITAEL AAA NK UniProtKB: Phytochrome A |
-Macromolecule #2: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...
Macromolecule | Name: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol- ...Name: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-yl)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid type: ligand / ID: 2 / Number of copies: 2 / Formula: O6E |
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Molecular weight | Theoretical: 586.678 Da |
Chemical component information | ChemComp-O6E: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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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 (6k x 4k) / Average electron dose: 50.0 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 |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 498817 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: PROJECTION MATCHING |