+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8474 | |||||||||
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Title | Cryo-EM structure of the human CTP synthase filament | |||||||||
Map data | Human CTP synthase filament | |||||||||
Sample |
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Function / homology | Function and homology information cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation / T cell proliferation / response to xenobiotic stimulus / ATP binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 6.1 Å | |||||||||
Authors | Lynch EM / Kollman JM | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: Human CTP synthase filament structure reveals the active enzyme conformation. Authors: Eric M Lynch / Derrick R Hicks / Matthew Shepherd / James A Endrizzi / Allison Maker / Jesse M Hansen / Rachael M Barry / Zemer Gitai / Enoch P Baldwin / Justin M Kollman / Abstract: The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we ...The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we show that for human CTPS, polymerization increases catalytic activity. The cryo-EM structures of bacterial and human CTPS filaments differ considerably in overall architecture and in the conformation of the CTPS protomer, explaining the divergent consequences of polymerization on activity. The structure of human CTPS filament, the first structure of the full-length human enzyme, reveals a novel active conformation. The filament structures elucidate allosteric mechanisms of assembly and regulation that rely on a conserved conformational equilibrium. The findings may provide a mechanism for increasing human CTPS activity in response to metabolic state and challenge the assumption that metabolic filaments are generally storage forms of inactive enzymes. Allosteric regulation of CTPS polymerization by ligands likely represents a fundamental mechanism underlying assembly of other metabolic filaments. | |||||||||
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_8474.map.gz | 201 MB | EMDB map data format | |
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Header (meta data) | emd-8474-v30.xml emd-8474.xml | 11.5 KB 11.5 KB | Display Display | EMDB header |
Images | emd_8474.png | 109.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8474 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8474 | HTTPS FTP |
-Related structure data
Related structure data | 5u03MC 8475C 8476C 8490C 8491C 8504C 8513C 5tkvC 5u05C 5u3cC 5u6rC C: citing same article (ref.) M: atomic model generated by this map |
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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_8474.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human CTP synthase filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.26 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 : human CTP synthase 1 filament
Entire | Name: human CTP synthase 1 filament |
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Components |
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-Supramolecule #1: human CTP synthase 1 filament
Supramolecule | Name: human CTP synthase 1 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pDO105-hCTPS1 |
-Macromolecule #1: CTP synthase 1
Macromolecule | Name: CTP synthase 1 / 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: Homo sapiens (human) |
Molecular weight | Theoretical: 66.777297 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDLD LGNYERFLDI RLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD AIQEWVMRQA LIPVDEDGLE PQVCVIELGG TVGDIESMPF I EAFRQFQF ...String: MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDLD LGNYERFLDI RLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD AIQEWVMRQA LIPVDEDGLE PQVCVIELGG TVGDIESMPF I EAFRQFQF KVKRENFCNI HVSLVPQPSS TGEQKTKPTQ NSVRELRGLG LSPDLVVCRC SNPLDTSVKE KISMFCHVEP EQ VICVHDV SSIYRVPLLL EEQGVVDYFL RRLDLPIERQ PRKMLMKWKE MADRYDRLLE TCSIALVGKY TKFSDSYASV IKA LEHSAL AINHKLEIKY IDSADLEPIT SQEEPVRYHE AWQKLCSAHG VLVPGGFGVR GTEGKIQAIA WARNQKKPFL GVCL GMQLA VVEFSRNVLG WQDANSTEFD PTTSHPVVVD MPEHNPGQMG GTMRLGKRRT LFQTKNSVMR KLYGDADYLE ERHRH RFEV NPVWKKCLEE QGLKFVGQDV EGERMEIVEL EDHPFFVGVQ YHPEFLSRPI KPSPPYFGLL LASVGRLSHY LQKGCR LSP RDTYSDRSGS SSPDSEITEL KFPSINHD |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #3: URIDINE 5'-TRIPHOSPHATE
Macromolecule | Name: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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 | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.9 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: Cylinder |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Helical parameters - Δz: 104.1 Å Applied symmetry - Helical parameters - Δ&Phi: 60.6 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: SPIDER, hsearch_lorentz, CTFFIND) / Number images used: 24880 |