[English] 日本語
Yorodumi
- EMDB-38855: GK tetramer of AtP5CS1 filament with adjacent hooks, reaction state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38855
TitleGK tetramer of AtP5CS1 filament with adjacent hooks, reaction state
Map data
Sample
  • Complex: Arabidopsis thaliana P5CSA incubated with all substrates.
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsL-proline biosynthesis / filamentous enzyme / TRANSFERASE / PLANT PROTEIN
Function / homology
Function and homology information


delta1-pyrroline-5-carboxylate synthetase activity / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / hyperosmotic salinity response / root development / L-proline biosynthetic process / response to water deprivation ...delta1-pyrroline-5-carboxylate synthetase activity / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / pollen development / hyperosmotic salinity response / root development / L-proline biosynthetic process / response to water deprivation / proline biosynthetic process / response to salt stress / chloroplast / response to oxidative stress / phosphorylation / Golgi apparatus / ATP binding / cytoplasm
Similarity search - Function
Delta l-pyrroline-5-carboxylate synthetase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Amino acid kinase family ...Delta l-pyrroline-5-carboxylate synthetase / GPR domain / Gamma-glutamyl phosphate reductase GPR, conserved site / Gamma-glutamyl phosphate reductase signature. / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Delta-1-pyrroline-5-carboxylate synthase A
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZhang T / Guo CJ / Liu JL
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Plants / Year: 2024
Title: Dynamic Arabidopsis P5CS filament facilitates substrate channelling.
Authors: Chen-Jun Guo / Tianyi Zhang / Qingqing Leng / Xian Zhou / Jiale Zhong / Ji-Long Liu /
Abstract: In plants, the rapid accumulation of proline is a common response to combat abiotic stress. Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalysing ...In plants, the rapid accumulation of proline is a common response to combat abiotic stress. Delta-1-pyrroline-5-carboxylate synthase (P5CS) is a rate-limiting enzyme in proline synthesis, catalysing the initial two-step conversion from glutamate to proline. Here we determine the first structure of plant P5CS. Our results show that Arabidopsis thaliana P5CS1 (AtP5CS1) and P5CS2 (AtP5CS2) can form enzymatic filaments in a substrate-sensitive manner. The destruction of AtP5CS filaments by mutagenesis leads to a significant reduction in enzymatic activity. Furthermore, separate activity tests on two domains reveal that filament-based substrate channelling is essential for maintaining the high catalytic efficiency of AtP5CS. Our study demonstrates the unique mechanism for the efficient catalysis of AtP5CS, shedding light on the intricate mechanisms underlying plant proline metabolism and stress response.
History
DepositionJan 26, 2024-
Header (metadata) releaseJun 5, 2024-
Map releaseJun 5, 2024-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_38855.png

Downloads & links

-
Map

FileDownload / File: emd_38855.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.6230273 - 3.4697092
Average (Standard dev.)0.018663837 (±0.09653258)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 254.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_38855_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_38855_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38855_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Arabidopsis thaliana P5CSA incubated with all substrates.

EntireName: Arabidopsis thaliana P5CSA incubated with all substrates.
Components
  • Complex: Arabidopsis thaliana P5CSA incubated with all substrates.
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Arabidopsis thaliana P5CSA incubated with all substrates.

SupramoleculeName: Arabidopsis thaliana P5CSA incubated with all substrates.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.9 kDa/nm

-
Macromolecule #1: Delta-1-pyrroline-5-carboxylate synthase A

MacromoleculeName: Delta-1-pyrroline-5-carboxylate synthase A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: glutamate 5-kinase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 78.993086 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH MEELDRSRAF ARDVKRIVVK VGTAVVTGKG GRLALGRLGA LCEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSS FADLQKPQTE LDGKACAGVG QSSLMAYYET MFDQLDVTAA QLLVNDSSFR DKDFRKQLNE TVKSMLDLRV I PIFNENDA ...String:
MGSSHHHHHH MEELDRSRAF ARDVKRIVVK VGTAVVTGKG GRLALGRLGA LCEQLAELNS DGFEVILVSS GAVGLGRQRL RYRQLVNSS FADLQKPQTE LDGKACAGVG QSSLMAYYET MFDQLDVTAA QLLVNDSSFR DKDFRKQLNE TVKSMLDLRV I PIFNENDA ISTRRAPYQD SSGIFWDNDS LAALLALELK ADLLILLSDV EGLYTGPPSD PNSKLIHTFV KEKHQDEITF GD KSRLGRG GMTAKVKAAV NAAYAGIPVI ITSGYSAENI DKVLRGLRVG TLFHQDARLW APITDSNARD MAVAARESSR KLQ ALSSED RKKILLDIAD ALEANVTTIK AENELDVASA QEAGLEESMV ARLVMTPGKI SSLAASVRKL ADMEDPIGRV LKKT EVADG LVLEKTSSPL GVLLIVFESR PDALVQIASL AIRSGNGLLL KGGKEARRSN AILHKVITDA IPETVGGKLI GLVTS REEI PDLLKLDDVI DLVIPRGSNK LVTQIKNTTK IPVLGHADGI CHVYVDKACD TDMAKRIVSD AKLDYPAACN AMETLL VHK DLEQNAVLNE LIFALQSNGV TLYGGPRASK ILNIPEARSF NHEYCAKACT VEVVEDVYGA IDHIHRHGSA HTDCIVT ED HEVAELFLRQ VDSAAVFHNA STRFSDGFRF GLGAEVGVST GRIHARGPVG VEGLLTTRWI MRGKGQVVDG DNGIVYTH Q DIPIQA

UniProtKB: Delta-1-pyrroline-5-carboxylate synthase A

-
Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
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: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wx3

Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 222855
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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://pdbjlvh1.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