+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23865 | |||||||||
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Title | Mouse CTPS2 bound to inhibitor R80 | |||||||||
Map data | Mouse CTPS2 bound to inhibitor R80 | |||||||||
Sample |
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Keywords | glutaminase / amidoligase / nucleotide metabolism / LIGASE | |||||||||
Function / homology | Function and homology information Interconversion of nucleotide di- and triphosphates / CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / mitochondrion / ATP binding ...Interconversion of nucleotide di- and triphosphates / CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / mitochondrion / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
Authors | Lynch EM / Dimattia MA | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2021 Title: Structural basis for isoform-specific inhibition of human CTPS1. Authors: Eric M Lynch / Michael A DiMattia / Steven Albanese / Gydo C P van Zundert / Jesse M Hansen / Joel D Quispe / Madison A Kennedy / Andreas Verras / Kenneth Borrelli / Angela V Toms / Neelu ...Authors: Eric M Lynch / Michael A DiMattia / Steven Albanese / Gydo C P van Zundert / Jesse M Hansen / Joel D Quispe / Madison A Kennedy / Andreas Verras / Kenneth Borrelli / Angela V Toms / Neelu Kaila / Kevin D Kreutter / Joshua J McElwee / Justin M Kollman / Abstract: Cytidine triphosphate synthase 1 (CTPS1) is necessary for an effective immune response, as revealed by severe immunodeficiency in CTPS1-deficient individuals [E. Martin ], [] [510], [288-292] ([2014]) ...Cytidine triphosphate synthase 1 (CTPS1) is necessary for an effective immune response, as revealed by severe immunodeficiency in CTPS1-deficient individuals [E. Martin ], [] [510], [288-292] ([2014]). CTPS1 expression is up-regulated in activated lymphocytes to expand CTP pools [E. Martin ], [] [510], [288-292] ([2014]), satisfying increased demand for nucleic acid and lipid synthesis [L. D. Fairbanks, M. Bofill, K. Ruckemann, H. A. Simmonds], [ ] [270], [29682-29689] ([1995]). Demand for CTP in other tissues is met by the CTPS2 isoform and nucleoside salvage pathways [E. Martin ], [] [510], [288-292] ([2014]). Selective inhibition of the proliferative CTPS1 isoform is therefore desirable in the treatment of immune disorders and lymphocyte cancers, but little is known about differences in regulation of the isoforms or mechanisms of known inhibitors. We show that CTP regulates both isoforms by binding in two sites that clash with substrates. CTPS1 is less sensitive to CTP feedback inhibition, consistent with its role in increasing CTP levels in proliferation. We also characterize recently reported small-molecule inhibitors, both CTPS1 selective and nonselective. Cryo-electron microscopy (cryo-EM) structures reveal these inhibitors mimic CTP binding in one inhibitory site, where a single amino acid substitution explains selectivity for CTPS1. The inhibitors bind to CTPS assembled into large-scale filaments, which for CTPS1 normally represents a hyperactive form of the enzyme [E. M. Lynch ], [] [24], [507-514] ([2017]). This highlights the utility of cryo-EM in drug discovery, particularly for cases in which targets form large multimeric assemblies not amenable to structure determination by other techniques. Both inhibitors also inhibit the proliferation of human primary T cells. The mechanisms of selective inhibition of CTPS1 lay the foundation for the design of immunosuppressive therapies. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23865.map.gz | 6.9 MB | EMDB map data format | |
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Header (meta data) | emd-23865-v30.xml emd-23865.xml | 11.9 KB 11.9 KB | Display Display | EMDB header |
Images | emd_23865.png | 198.4 KB | ||
Filedesc metadata | emd-23865.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23865 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23865 | HTTPS FTP |
-Validation report
Summary document | emd_23865_validation.pdf.gz | 377.4 KB | Display | EMDB validaton report |
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Full document | emd_23865_full_validation.pdf.gz | 376.9 KB | Display | |
Data in XML | emd_23865_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_23865_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23865 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23865 | HTTPS FTP |
-Related structure data
Related structure data | 7miuMC 7mgzC 7mh0C 7mh1C 7mifC 7migC 7mihC 7miiC 7mipC 7mivC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23865.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mouse CTPS2 bound to inhibitor R80 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : mCTPS2 tetramer
Entire | Name: mCTPS2 tetramer |
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Components |
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-Supramolecule #1: mCTPS2 tetramer
Supramolecule | Name: mCTPS2 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: CTP synthase 2
Macromolecule | Name: CTP synthase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing) |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 65.59225 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MKYILVTGGV ISGIGKGIIA SSIGTILKSC GLRVTAIKID PYINIDAGTF SPYEHGEVFV LNDGGEVDLD LGNYERFLDI NLYKDNNIT TGKIYQHVIN KERRGDYLGK TVQVVPHITD AIQEWVMNQA KVSVDGNKED PQICVIELGG TIGDIEGMAF V EAFRQFQF ...String: MKYILVTGGV ISGIGKGIIA SSIGTILKSC GLRVTAIKID PYINIDAGTF SPYEHGEVFV LNDGGEVDLD LGNYERFLDI NLYKDNNIT TGKIYQHVIN KERRGDYLGK TVQVVPHITD AIQEWVMNQA KVSVDGNKED PQICVIELGG TIGDIEGMAF V EAFRQFQF KAKKENFYNI HVSLVPQPSA TGEQKTKPTQ NSVRALRGLG LSPDLIVCRS STPIEMAVKE KISMFCHVNP EQ VICIHDV SSIYRVPLLL EEQGVVKYFQ ERLGLPINDC SSNLLFKWKA MADRYERLQK ICSIALVGKY TKLRDCYASV FKA LEHSAL AINHKLNLMY IDSIDLEPVT KAEDPVKFHE AWQKLCLADG ILVPGGFGIR GTLGKLQAIS WARTKKIPFL GICL GMQLA VIEFARNCLN LKDANSTEFE PNTPVPLVID MPEHNPGDLG GTMRLGLRRT VFTTENSILK KLYGDVPYIE ERHRH RYEV NPNLINQFEN KDLCFVGEDV DGKRMEIVEL TSHPYFIGVQ FHPEFSSRPM KPSPPYLGLL LAATGNLNAH LQQMNK LPY SDGYSDASDD SFPEAKLAEL DLN UniProtKB: CTP synthase 2 |
-Macromolecule #2: GLUTAMINE
Macromolecule | Name: GLUTAMINE / type: ligand / ID: 2 / Number of copies: 4 / Formula: GLN |
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Molecular weight | Theoretical: 146.144 Da |
Chemical component information | ChemComp-GLN: |
-Macromolecule #3: N-(1-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}cyclopropy...
Macromolecule | Name: N-(1-{2-[(cyclopropanesulfonyl)amino]-1,3-thiazol-4-yl}cyclopropyl)-5-(6-ethoxypyrazin-2-yl)pyridine-2-carboxamide type: ligand / ID: 3 / Number of copies: 4 / Formula: ZG4 |
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Molecular weight | Theoretical: 486.567 Da |
Chemical component information | ChemComp-ZG4: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #5: URIDINE 5'-TRIPHOSPHATE
Macromolecule | Name: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: UTP |
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Molecular weight | Theoretical: 484.141 Da |
Chemical component information | ChemComp-UTP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 155211 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |