[English] 日本語
Yorodumi
- EMDB-8513: E. coli CTP synthase CC mutant filament (product-bound) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8513
TitleE. coli CTP synthase CC mutant filament (product-bound)
Map dataE. coli CTP synthase CC mutant filament (product-bound)
Sample
  • Complex: E. coli CTP synthase CC mutant filament
    • Protein or peptide: CTP synthaseCTP synthetase
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / magnesium ion binding / protein-containing complex / ATP binding ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / magnesium ion binding / protein-containing complex / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
CTP synthase / CTP synthase N-terminus / CTP synthase GATase domain / CTP synthase, N-terminal / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Glutamine amidotransferase / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CTP synthase / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodhelical reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsKollman JM / Lynch EM
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.
History
DepositionDec 8, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseApr 26, 2017-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5u6r
  • Surface level: 2.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_8513.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli CTP synthase CC mutant filament (product-bound)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 200 pix.
= 252. Å
1.26 Å/pix.
x 200 pix.
= 252. Å
1.26 Å/pix.
x 200 pix.
= 252. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 2.1 / Movie #1: 2.1
Minimum - Maximum-3.784991 - 7.626205
Average (Standard dev.)0.000000000183376 (±0.60962296)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 252.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z252.000252.000252.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS200200200
D min/max/mean-3.7857.6260.000

-
Supplemental data

-
Sample components

-
Entire : E. coli CTP synthase CC mutant filament

EntireName: E. coli CTP synthase CC mutant filament
Components
  • Complex: E. coli CTP synthase CC mutant filament
    • Protein or peptide: CTP synthaseCTP synthetase
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

-
Supramolecule #1: E. coli CTP synthase CC mutant filament

SupramoleculeName: 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
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET22b

-
Macromolecule #1: CTP synthase

MacromoleculeName: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing)
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 60.44698 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

MacromoleculeName: CYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: CTP
Molecular weightTheoretical: 483.156 Da
Chemical component information

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate

-
Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.15 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE
DetailsFilaments 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

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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

CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER / Details: Cylinder
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER
Final reconstructionApplied 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more