[English] 日本語
Yorodumi
- EMDB-35693: Pr conformer of Zea mays phytochrome A1 - ZmphyA1-Pr -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35693
TitlePr conformer of Zea mays phytochrome A1 - ZmphyA1-Pr
Map data
Sample
  • Complex: Zea mays phytochrome A1 (ZmphyA1-Pr)
    • Protein or peptide: Phytochrome
  • Ligand: 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
Keywordsmaize phytochrome A1 / Pr conformer / far-red light receptor / PLANT PROTEIN
Function / homology
Function and homology information


red, far-red light phototransduction / detection of visible light / phosphorelay sensor kinase activity / photoreceptor activity / regulation of DNA-templated transcription / protein homodimerization activity / nucleus
Similarity search - Function
Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain ...Phytochrome A/B/C/D/E / Phytochrome chromophore binding site / Phytochrome chromophore attachment site signature. / Phytochrome / Phytochrome, PHY domain superfamily / Phytochrome, central region / PAS fold-2 / PAS fold / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Histidine kinase domain / Histidine kinase domain profile. / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress) / Zea mays (maize)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang Y / Ma C / Zhao J / Gao N / Wang J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionMar 20, 2023-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_35693.png

Downloads & links

-
Map

FileDownload / File: emd_35693.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.)
0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å		0.85 Å/pix.
x 320 pix.
= 272. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.68871117 - 1.0865606
Average (Standard dev.)0.000072731025 (±0.020370146)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_35693_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_35693_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Zea mays phytochrome A1 (ZmphyA1-Pr)

EntireName: Zea mays phytochrome A1 (ZmphyA1-Pr)
Components
  • Complex: Zea mays phytochrome A1 (ZmphyA1-Pr)
    • Protein or peptide: Phytochrome
  • Ligand: 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

-
Supramolecule #1: Zea mays phytochrome A1 (ZmphyA1-Pr)

SupramoleculeName: Zea mays phytochrome A1 (ZmphyA1-Pr) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Macromolecule #1: Phytochrome

MacromoleculeName: Phytochrome / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Zea mays (maize)
Molecular weightTheoretical: 124.72643 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSSLRPAQSS SSSSRTRQSS QARILAQTTL DAELNAEYEE SGDSFDYSKL VEAQRSTPPE QQGRSGKVIA YLQHIQRGKL IQPFGCLLA LDEKSFRVIA FSENAPEMLT TVSHAVPNVD DPPKLGIGTN VRSLFTDPGA TALQKALGFA DVSLLNPILV Q CKTSGKPF ...String:
MSSLRPAQSS SSSSRTRQSS QARILAQTTL DAELNAEYEE SGDSFDYSKL VEAQRSTPPE QQGRSGKVIA YLQHIQRGKL IQPFGCLLA LDEKSFRVIA FSENAPEMLT TVSHAVPNVD DPPKLGIGTN VRSLFTDPGA TALQKALGFA DVSLLNPILV Q CKTSGKPF YAIVHRATGC LVVDFEPVKP TEFPATAAGA LQSYKLAAKA ISKIQSLPGG SMQALCNTVV KEVFDLTGYD RV MAYKFHE DEHGEVFAEI TKPGIEPYLG LHYPATDIPQ AARFLFMKNK VRMICDCRAR SVKIIEDEAL SIDISLCGST LRA PHSCHL QYMENMNSIA SLVMAVVVNE NEDDDEPESE QPPQQQKRKK LWGLIVCHHE SPRYVPFPLR YACEFLAQVF AVHV NKEFE LEKQIREKSI LRMQTMLSDM LFKESSPLSI VSGSPNIMDL VKCDGAALLY GDKVWRLQTA PTESQIRDIA FWLSE VHGD STGLSTDSLQ DAGYPGAASL GDMICGMAVA KITSKDILFW FRSHTAAEIK WGGAKHDPSD EDDSRRMHPR LSFKAF LEV VKMKSLPWSD YEMDAIHSLQ LILRGTLNDA LKPAQSSGLD NQIGDLKLDG LAELQAVTSE MVRLMETATV PILAVDG NG LVNGWNQKVA DLSGLRVDEA IGRHILTLVE DSSVPIVQRM LYLALQGREE KEVRFELKTH GSKRDDGPVI LVVNACAS R DMHDHVVGVC FVAQDMTVHK LVMDKFTRVE GDYRAIIHNP NPLIPPIFGA DQFGWCSEWN AAMTKLTGWH RDEVIDRML LGEVFDSSNA SCLLKSKDAF VRLCIIINSA LAGEEAEKAP IGFFDRDGKY IECLLSVNRK VNADGVVTGV FCFIHVPSDD LQHALHVQQ ASEQTALRRL KAFSYMRHAI DKPLSGMLYS RETLKGTDLD EEQMRQVRVA DNCHRQLNKI LADLDQDNIT D KSSCLDLD MAEFVLQDVV VSAVSQVLIG CQGKGIRVAC NLPERSMKQK VYGDGIRLQQ ILSDFLFVSV KFSPAGGSVD IS SKLTKNS IGENLHLIDF ELRIKHQGAG VPAEILSQMY GEDNREQSEE GLSLLVSRNL LRLMNGDIRH LREAGMSTFI LTA ELAAA

UniProtKB: Phytochrome

-
Macromolecule #2: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydro...

MacromoleculeName: 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
Molecular weightTheoretical: 586.678 Da
Chemical component information

ChemComp-O6E:
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 229726
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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