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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr | |||||||||
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![]() | phytochrome A / Pr conformer / far-red light receptor / PLANT PROTEIN | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Zhang Y / Ma C / Zhao J / Gao N / Wang J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 117.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.9 KB 15.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.5 KB | Display | ![]() |
Images | ![]() | 35.1 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Others | ![]() ![]() | 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 992.5 KB | Display | ![]() |
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Full document | ![]() | 992 KB | Display | |
Data in XML | ![]() | 19 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8isjMC ![]() 8isiC ![]() 8iskC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
-Half map: #2
File | emd_35692_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_35692_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr
Entire | Name: Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr |
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Components |
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-Supramolecule #1: Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr
Supramolecule | Name: Pr conformer of Arabidopsis thaliana phytochrome A - AtphyA-Pr type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 124.409492 KDa |
Recombinant expression | Organism: Insect cell expression vector pTIE1 (others) |
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 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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |