[English] 日本語
Yorodumi
- PDB-5u03: Cryo-EM structure of the human CTP synthase filament -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5u03
TitleCryo-EM structure of the human CTP synthase filament
ComponentsCTP synthase 1
KeywordsLIGASE / PROTEIN FIBRIL / nucleotide metabolism / enzyme / filament
Function/homologyCTP synthase / CTP synthase activity / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / CTP synthase N-terminus / 'de novo' CTP biosynthetic process / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase / B cell proliferation ...CTP synthase / CTP synthase activity / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / CTP synthase N-terminus / 'de novo' CTP biosynthetic process / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase / B cell proliferation / CTP biosynthetic process / Glutamine amidotransferase class-I / nucleobase-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / glutamine metabolic process / T cell proliferation / nucleobase-containing small molecule interconversion / Class I glutamine amidotransferase-like / response to drug / P-loop containing nucleoside triphosphate hydrolase / membrane / ATP binding / identical protein binding / cytosol / CTP synthase 1
Function and homology information
Specimen sourceHomo sapiens / / human
MethodElectron microscopy (6.1 Å resolution / Filament / Helical) / Transmission electron microscopy
AuthorsLynch, E.M. / Kollman, J.M.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 22, 2016 / Release: Apr 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 26, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Jun 21, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Movie
  • Biological unit as representative helical assembly
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer

Downloads & links

-
Assembly

Deposited unit
A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,07412
Polyers267,1094
Non-polymers3,9658
Water0
1
A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules

A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules

A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules

A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,084,29848
Polyers1,068,43716
Non-polymers15,86132
Water0
TypeNameSymmetry operationNumber
helical symmetry operation4
2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 4 / Rise per n subunits: 104.1 Å / Rotation per n subunits: 60.6 deg.

-
Components

#1: Protein/peptide
CTP synthase 1 / CTP synthetase 1 / UTP--ammonia ligase 1


Mass: 66777.297 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens / / human / Gene: CTPS1, CTPS / Production host: Saccharomyces cerevisiae / References: UniProt:P17812, EC:6.3.4.2 (CTP synthase)
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / : Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 4 / Formula: C9H15N2O15P3 / : Uridine triphosphate / Comment: UTP *YM

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: HELICAL

-
Sample preparation

ComponentName: human CTP synthase 1 filament / Type: COMPLEX
Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP
Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens
Source (recombinant)Organism: Saccharomyces cerevisiae / Plasmid: pDO105-hCTPS1
Buffer solutionpH: 7.9
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

-
Processing

EM software
IDNameCategory
13SPIDERRECONSTRUCTION
14hsearch_lorentzRECONSTRUCTION
15ctffindRECONSTRUCTION
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 60.6 deg. / Axial rise/subunit: 104.1 Å / Axial symmetry: C1
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24880 / Symmetry type: HELICAL

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more