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Open data
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Basic information
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Title | Drosophila P5CS filament with glutamate, ATP, and NADPH | |||||||||
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![]() | filament / ALDH18A1 / Delta-1-pyrroline-5-carboxylate synthase / BIOSYNTHETIC PROTEIN / TRANSFERASE | |||||||||
Function / homology | ![]() 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 / phosphorylation / mitochondrion / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Liu JL / Zhong J | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 12.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.7 KB 13.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.7 KB | Display | ![]() |
Images | ![]() | 86.1 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Filedesc metadata | ![]() | 5.5 KB | ||
Others | ![]() ![]() | 78.8 MB 78.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 782.5 KB | Display | ![]() |
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Full document | ![]() | 782.1 KB | Display | |
Data in XML | ![]() | 17.7 KB | Display | |
Data in CIF | ![]() | 23.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f5vMC ![]() 7f5tC ![]() 7f5uC ![]() 7f5xC ![]() 7wx3C ![]() 7wx4C ![]() 7wxfC ![]() 7wxgC ![]() 7wxhC ![]() 7wxiC 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: 1.06 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Half map: #1
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-Half map: #2
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Sample components
-Entire : Drosophila Delta-1-pyrroline-5-carboxylate synthase in reaction
Entire | Name: Drosophila Delta-1-pyrroline-5-carboxylate synthase in reaction |
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Components |
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-Supramolecule #1: Drosophila Delta-1-pyrroline-5-carboxylate synthase in reaction
Supramolecule | Name: Drosophila Delta-1-pyrroline-5-carboxylate synthase in reaction type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Delta-1-pyrroline-5-carboxylate synthase
Macromolecule | Name: Delta-1-pyrroline-5-carboxylate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glutamate 5-kinase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 84.198227 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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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) / Detector mode: SUPER-RESOLUTION / Average electron dose: 72.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |