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Yorodumi- EMDB-35691: Photochromobilin-free form of Arabidopsis thaliana phytochrome A ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35691 | |||||||||
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Title | Photochromobilin-free form of Arabidopsis thaliana phytochrome A - apo-AtphyA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | phytochrome A / Photochromobilin-free form / far-red light receptor / PLANT PROTEIN | |||||||||
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 / negative regulation of translation / nuclear body / 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: 3.77 Å | |||||||||
Authors | Zhang Y / Ma C / Zhao J / Gao N / Wang J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2023 Title: Structural insights into plant phytochrome A as a highly sensitized photoreceptor. Authors: Yuxuan Zhang / Xiaoli Lin / Chengying Ma / Jun Zhao / Xiaojin Shang / Zhengdong Wang / Bin Xu / Ning Gao / Xing Wang Deng / Jizong Wang / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35691.map.gz | 3 MB | EMDB map data format | |
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Header (meta data) | emd-35691-v30.xml emd-35691.xml | 15.4 KB 15.4 KB | Display Display | EMDB header |
Images | emd_35691.png | 33.1 KB | ||
Filedesc metadata | emd-35691.cif.gz | 6 KB | ||
Others | emd_35691_half_map_1.map.gz emd_35691_half_map_2.map.gz | 45.2 MB 45.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35691 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35691 | HTTPS FTP |
-Validation report
Summary document | emd_35691_validation.pdf.gz | 686.6 KB | Display | EMDB validaton report |
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Full document | emd_35691_full_validation.pdf.gz | 686.2 KB | Display | |
Data in XML | emd_35691_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_35691_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35691 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35691 | HTTPS FTP |
-Related structure data
Related structure data | 8isiMC 8isjC 8iskC 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_35691.map.gz / Format: CCP4 / Size: 52.7 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: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35691_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35691_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Photochromobilin-free form of Arabidopsis thaliana phytochrome A ...
Entire | Name: Photochromobilin-free form of Arabidopsis thaliana phytochrome A (apo-AtphyA) |
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Components |
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-Supramolecule #1: Photochromobilin-free form of Arabidopsis thaliana phytochrome A ...
Supramolecule | Name: Photochromobilin-free form of Arabidopsis thaliana phytochrome A (apo-AtphyA) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Arabidopsis thaliana (thale cress) |
Molecular weight | Theoretical: 125.17143 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
Sequence | String: MEKKMSGSRP TQSSEGSRRS RHSARIIAQT TVDAKLHADF EESGSSFDYS TSVRVTGPVV ENQPPRSDKV TTTYLHHIQK GKLIQPFGC LLALDEKTFK VIAYSENASE LLTMASHAVP SVGEHPVLGI GTDIRSLFTA PSASALQKAL GFGDVSLLNP I LVHCRTSA ...String: MEKKMSGSRP TQSSEGSRRS RHSARIIAQT TVDAKLHADF EESGSSFDYS TSVRVTGPVV ENQPPRSDKV TTTYLHHIQK GKLIQPFGC LLALDEKTFK VIAYSENASE LLTMASHAVP SVGEHPVLGI GTDIRSLFTA PSASALQKAL GFGDVSLLNP I LVHCRTSA KPFYAIIHRV TGSIIIDFEP VKPYEVPMTA AGALQSYKLA AKAITRLQSL PSGSMERLCD TMVQEVFELT GY DRVMAYK FHEDDHGEVV SEVTKPGLEP YLGLHYPATD IPQAARFLFM KNKVRMIVDC NAKHARVLQD EKLSFDLTLC GST LRAPHS CHLQYMANMD SIASLVMAVV VNEEDGEGDA PDATTQPQKR KRLWGLVVCH NTTPRFVPFP LRYACEFLAQ VFAI HVNKE VELDNQMVEK NILRTQTLLC DMLMRDAPLG IVSQSPNIMD LVKCDGAALL YKDKIWKLGT TPSEFHLQEI ASWLC EYHM DSTGLSTDSL HDAGFPRALS LGDSVCGMAA VRISSKDMIF WFRSHTAGEV RWGGAKHDPD DRDDARRMHP RSSFKA FLE VVKTRSLPWK DYEMDAIHSL QLILRNAFKD SETTDVNTKV IYSKLNDLKI DGIQELEAVT SEMVRLIETA TVPILAV DS DGLVNGWNTK IAELTGLSVD EAIGKHFLTL VEDSSVEIVK RMLENALEGT EEQNVQFEIK THLSRADAGP ISLVVNAC A SRDLHENVVG VCFVAHDLTG QKTVMDKFTR IEGDYKAIIQ NPNPLIPPIF GTDEFGWCTE WNPAMSKLTG LKREEVIDK MLLGEVFGTQ KSCCRLKNQE AFVNLGIVLN NAVTSQDPEK VSFAFFTRGG KYVECLLCVS KKLDREGVVT GVFCFLQLAS HELQQALHV QRLAERTAVK RLKALAYIKR QIRNPLSGIM FTRKMIEGTE LGPEQRRILQ TSALCQKQLS KILDDSDLES I IEGCLDLE MKEFTLNEVL TASTSQVMMK SNGKSVRITN ETGEEVMSDT LYGDSIRLQQ VLADFMLMAV NFTPSGGQLT VS ASLRKDQ LGRSVHLANL EIRLTHTGAG IPEFLLNQMF GTEEDVSEEG LSLMVSRKLV KLMNGDVQYL RQAGKSSFII TAE LAAANK UniProtKB: Phytochrome A |
-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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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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 873442 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |