[English] 日本語
Yorodumi
- EMDB-28871: CryoEM structure of Arabidopsis thaliana phytochrome A (focused m... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-28871
TitleCryoEM structure of Arabidopsis thaliana phytochrome A (focused map of platform)
Map data
Sample
  • Complex: phytochrome A
    • Protein or peptide: Phytochrome A
KeywordsPhytochrome / asymmetric dimer / gene regulation
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLi H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: Nat Plants / Year: 2023
Title: The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms.
Authors: E Sethe Burgie / Hua Li / Zira T K Gannam / Katrice E McLoughlin / Richard D Vierstra / Huilin Li /
Abstract: Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The ...Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception.
History
DepositionNov 15, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateAug 2, 2023-
Current statusAug 2, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_28871.png

Downloads & links

-
Map

FileDownload / File: emd_28871.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å		0.83 Å/pix.
x 320 pix.
= 264.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.162
Minimum - Maximum-3.7136323 - 6.146827
Average (Standard dev.)0.001413372 (±0.09867807)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_28871_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_28871_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_28871_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : phytochrome A

EntireName: phytochrome A
Components
  • Complex: phytochrome A
    • Protein or peptide: Phytochrome A

-
Supramolecule #1: phytochrome A

SupramoleculeName: phytochrome A / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 249 KDa

-
Macromolecule #1: Phytochrome A

MacromoleculeName: Phytochrome A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
SequenceString: GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH CRTSAKPFYA ...String:
GMSGSRPTQS SEGSRRSRHS ARIIAQTTVD AKLHADFEES GSSFDYSTSV RVTGPVVENQ PPRSDKVTTT YLHHIQKGKL IQPFGCLLAL DEKTFKVIAY SENASELLTM ASHAVPSVGE HPVLGIGTDI RSLFTAPSAS ALQKALGFGD VSLLNPILVH CRTSAKPFYA IIHRVTGSII IDFEPVKPYE VPMTAAGALQ SYKLAAKAIT RLQSLPSGSM ERLCDTMVQE VFELTGYDRV MAYKFHEDDH GEVVSEVTKP GLEPYLGLHY PATDIPQAAR FLFMKNKVRM IVDCNAKHAR VLQDEKLSFD LTLCGSTLRA PHSCHLQYMA NMDSIASLVM AVVVNEEDGE GDAPDATTQP QKRKRLWGLV VCHNTTPRFV PFPLRYACEF LAQVFAIHVN KEVELDNQMV EKNILRTQTL LCDMLMRDAP LGIVSQSPNI MDLVKCDGAA LLYKDKIWKL GTTPSEFHLQ EIASWLCEYH MDSTGLSTDS LHDAGFPRAL SLGDSVCGMA AVRISSKDMI FWFRSHTAGE VRWGGAKHDP DDRDDARRMH PRSSFKAFLE VVKTRSLPWK DYEMDAIHSL QLILRNAFKD SETTDVNTKV IYSKLNDLKI DGIQELEAVT SEMVRLIETA TVPILAVDSD GLVNGWNTKI AELTGLSVDE AIGKHFLTLV EDSSVEIVKR MLENALEGTE EQNVQFEIKT HLSRADAGPI SLVVNACASR DLHENVVGVC FVAHDLTGQK TVMDKFTRIE GDYKAIIQNP NPLIPPIFGT DEFGWCTEWN PAMSKLTGLK REEVIDKMLL GEVFGTQKSC CRLKNQEAFV NLGIVLNNAV TSQDPEKVSF AFFTRGGKYV ECLLCVSKKL DREGVVTGVF CFLQLASHEL QQALHVQRLA ERTAVKRLKA LAYIKRQIRN PLSGIMFTRK MIEGTELGPE QRRILQTSAL CQKQLSKILD DSDLESIIEG CLDLEMKEFT LNEVLTASTS QVMMKSNGKS VRITNETGEE VMSDTLYGDS IRLQQVLADF MLMAVNFTPS GGQLTVSASL RKDQLGRSVH LANLEIRLTH TGAGIPEFLL NQMFGTEEDV SEEGLSLMVS RKLVKLMNGD VQYLRQAGKS SFIITAELAA ANK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
75.0 mMKClpotassium chloride
20.0 mMC9H20N2O4SHEPES
10.0 mMC2H6OS2-Mercaptoethanol
0.01 mMC10H16N2O8EDTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 299 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 193.0 K / Max: 193.0 K
Alignment procedureComa free - Residual tilt: 0.05 mrad
Image recordingFilm 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: 6390 / Average exposure time: 1.0 sec. / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 3777726
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 421968
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more