+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8513 | |||||||||
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Title | E. coli CTP synthase CC mutant filament (product-bound) | |||||||||
Map data | E. coli CTP synthase CC mutant filament (product-bound) | |||||||||
Sample |
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Function / homology | Function and homology information CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding ...CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 5.7 Å | |||||||||
Authors | Kollman JM / Lynch EM | |||||||||
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_8513.map.gz | 28.1 MB | EMDB map data format | |
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Header (meta data) | emd-8513-v30.xml emd-8513.xml | 11.8 KB 11.8 KB | Display Display | EMDB header |
Images | emd_8513.png | 63.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8513 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8513 | HTTPS FTP |
-Validation report
Summary document | emd_8513_validation.pdf.gz | 459.1 KB | Display | EMDB validaton report |
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Full document | emd_8513_full_validation.pdf.gz | 458.6 KB | Display | |
Data in XML | emd_8513_validation.xml.gz | 5.9 KB | Display | |
Data in CIF | emd_8513_validation.cif.gz | 6.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8513 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8513 | HTTPS FTP |
-Related structure data
Related structure data | 5u6rMC 8474C 8475C 8476C 8490C 8491C 8504C 5tkvC 5u03C 5u05C 5u3cC 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_8513.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | E. coli CTP synthase CC mutant filament (product-bound) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : E. coli CTP synthase CC mutant filament
Entire | Name: E. coli CTP synthase CC mutant filament |
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Components |
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-Supramolecule #1: E. coli CTP synthase CC mutant filament
Supramolecule | Name: E. coli CTP synthase CC mutant filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Disulfide-crosslinked E. coli CTP synthase filaments assembled in non-reducing buffer, bound to CTP and ADP |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET22b |
-Macromolecule #1: CTP synthase
Macromolecule | Name: CTP synthase / 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: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 60.44698 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MTTNYIFVTG GVVSSLGKGI AAASLAAILE ARGLNVTIMK LDPYINVDPG TMSPIQHGEV FVTEDGAETD LDLGHYERFI RTKMSRRNN FTTGRIYSDV LRKERRGDYL GATVQVIPHI TNAIKERVLE GGEGHDVVLV EIGGTVGDIE SLPFLEAIRQ M AVEIGREH ...String: MTTNYIFVTG GVVSSLGKGI AAASLAAILE ARGLNVTIMK LDPYINVDPG TMSPIQHGEV FVTEDGAETD LDLGHYERFI RTKMSRRNN FTTGRIYSDV LRKERRGDYL GATVQVIPHI TNAIKERVLE GGEGHDVVLV EIGGTVGDIE SLPFLEAIRQ M AVEIGREH TLFMHLTLVP YMAASGEVKT KPTQHSVKEL LSIGIQPDIL ICRSDRAVPA NERAKIALFC NVPEKAVISL KD VDSIYKI PGLLKSQGLD DYICKRFSLN CPEANLSEWE QVIFEEANPV SEVTIGMVGK YIELPDAYKS VIEALKHGGL KNR VSVNIK LIDSQDVETR GVEILKGLDA ILVPGGFGYR GVEGMITTAR FARENNIPYL GICLGMQVAL IDYARHVANM ENAN STEFV PDCKYPVVAL ITEWRDENGN VEVRSEKSDL GGTMRLGAQQ CQLVDDSLVR QLYNAPTIVE RHRHRYEVNN MLLKQ IEDA GLRVAGRSGD DQLVEIIEVP NHPWFVACQF HPEFTSTPRD GHPLFAGFVK AASEFQKRQA K |
-Macromolecule #2: CYTIDINE-5'-TRIPHOSPHATE
Macromolecule | Name: CYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CTP |
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Molecular weight | Theoretical: 483.156 Da |
Chemical component information | ChemComp-CTP: |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
Details | Filaments were assembled by dialysis in non-reducing buffer (50 mM Na-HEPES, pH 8.0). Products CTP (0.6 mM) and ADP (1.5 mM) were added to filaments. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 82.1 Å Applied symmetry - Helical parameters - Δ&Phi: 48.2 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: SPIDER, hsearch_lorentz) / Number images used: 31170 |
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CTF correction | Software - Name: CTFFIND |
Startup model | Type of model: OTHER / Details: Cylinder |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: SPIDER |