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- EMDB-31467: Drosophila P5CS filament with glutamate and ATPgammaS -

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Basic information

Entry
Database: EMDB / ID: EMD-31467
TitleDrosophila P5CS filament with glutamate and ATPgammaS
Map data
Sample
  • Organelle or cellular component: Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with ATP-gamma-S and Glutamate
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase
Keywordsfilament / ALDH18A1 / Delta-1-pyrroline-5-carboxylate synthase / BIOSYNTHETIC PROTEIN / TRANSFERASE
Function / homology
Function and homology information


Glutamate and glutamine metabolism / Mitochondrial protein degradation / glutamate-5-semialdehyde dehydrogenase / glutamate-5-semialdehyde dehydrogenase activity / glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / proline biosynthetic process / mitochondrion / ATP binding
Similarity search - Function
Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / 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 ...Bifunctional delta 1-pyrroline-5-carboxylate synthetase, glutamate-5-kinase domain / 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 / Acetylglutamate kinase-like superfamily / Amino acid kinase family / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Delta-1-pyrroline-5-carboxylate synthase
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLiu JL / Zhong J
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Elife / Year: 2022
Title: Structural basis of dynamic P5CS filaments.
Authors: Jiale Zhong / Chen-Jun Guo / Xian Zhou / Chia-Chun Chang / Boqi Yin / Tianyi Zhang / Huan-Huan Hu / Guang-Ming Lu / Ji-Long Liu /
Abstract: The bifunctional enzyme Δ-pyrroline-5-carboxylate synthase (P5CS) is vital to the synthesis of proline and ornithine, playing an essential role in human health and agriculture. Pathogenic mutations ...The bifunctional enzyme Δ-pyrroline-5-carboxylate synthase (P5CS) is vital to the synthesis of proline and ornithine, playing an essential role in human health and agriculture. Pathogenic mutations in the P5CS gene (ALDH18A1) lead to neurocutaneous syndrome and skin relaxation connective tissue disease in humans, and P5CS deficiency seriously damages the ability to resist adversity in plants. We have recently found that P5CS forms cytoophidia in vivo and filaments in vitro. However, it is difficult to appreciate the function of P5CS filamentation without precise structures. Using cryo-electron microscopy, here we solve the structures of full-length P5CS in three states at resolution from 3.1 to 4.3 Å. We observe distinct ligand-binding states and conformational changes for the GK and GPR domains, respectively. Divergent helical filaments are assembled by P5CS tetramers and stabilized by multiple interfaces. Point mutations disturbing those interfaces prevent P5CS filamentation and greatly reduce the enzymatic activity. Our findings reveal that filamentation is crucial for the coordination between the GK and GPR domains, providing a structural basis for the catalytic function of P5CS filaments.
History
DepositionJun 22, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31467.png

Downloads & links

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Map

FileDownload / File: emd_31467.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å		1.06 Å/pix.
x 300 pix.
= 318. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.020086506 - 0.046980202
Average (Standard dev.)0.0003008692 (±0.0017363417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with AT...

EntireName: Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with ATP-gamma-S and Glutamate
Components
  • Organelle or cellular component: Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with ATP-gamma-S and Glutamate
    • Protein or peptide: Delta-1-pyrroline-5-carboxylate synthase

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Supramolecule #1: Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with AT...

SupramoleculeName: Drosophila Delta-1-pyrroline-5-carboxylate synthase bound with ATP-gamma-S and Glutamate
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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

MacromoleculeName: Delta-1-pyrroline-5-carboxylate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glutamate 5-kinase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 84.198227 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MLQNSFKLAQ SLRNGFYRNA WRAFSSHGPR QPLVSPERRL EKAHPTFTER SQLKYARRLV VKLGSAVITR EDNHGLALGR LASIVEQVA ECHLEGREVM MVTSGAVAFG KQKLAQELLM SLSMRETLNP KDSKEFDGAT LEPRAAAAVG QSGLMSLYDA M FAQYGVKI ...String:
MLQNSFKLAQ SLRNGFYRNA WRAFSSHGPR QPLVSPERRL EKAHPTFTER SQLKYARRLV VKLGSAVITR EDNHGLALGR LASIVEQVA ECHLEGREVM MVTSGAVAFG KQKLAQELLM SLSMRETLNP KDSKEFDGAT LEPRAAAAVG QSGLMSLYDA M FAQYGVKI AQVLVTKPDF YNEETRNNLF CTLSELISLN IVPIINTNDA VSPPMFIRDD EPAGGARRGI PIKDNDSLSA ML AAEVQAD LLILMSDVDG IYNKPPWEDG AKLMHTYTSD DSNSIEFGKK SKVGTGGMDS KVKAATWALD RGVSVVICNG MQE KAIKTI IGGRKVGTFF TEATESANAV PVEVMAENAR TGSRQMQALT PAQRASAVNT LADLLVSREK FILDANAKDL AEAQ KSGLA KPLLSRLSLN PAKLKNLSVG LKQIAEDSHK NVGRVLRRTR LADQLELKQV TVPIGVLLVI FESRPDSLPQ VAALA MASA NGLLLKGGKE AAHSNKALME LVKEALATVG AEHAVSLVST REEISDLLSM ENHIDLIIPR GSSDLVRSIQ QQSLHI PVL GHAEGVCHVY IDRDADLEKA LRIARDAKCD YPAACNAMET LLIHEDLMSG AIFGDVCNML KREGVKIYAG PRLNQQL TF GPPAAKSLKH EYGALECCIE VVPSLDEAIN HIHTYGSSHT DVIVTENDAA ARQFLGSVDS ACVFHNASSR FADGFRFG L GAEVGISTAR IHARGPVGVE GLLTTKWILE GQDHAAADFA EGGGRTWLHE TLPLD

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 72.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 292974
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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