[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
DescriptorCTP synthase 1 (E.C.6.3.4.2)
KeywordsLIGASE / PROTEIN FIBRIL / nucleotide metabolism / enzyme / filament
Specimen sourceHomo sapiens / human
MethodElectron microscopy (6.1 Å resolution / Filament / Helical)
AuthorsLynch, E.M. / Kollman, J.M.
CitationNat. Struct. Mol. Biol., 2017, 24, 507-514

Nat. Struct. Mol. Biol., 2017, 24, 507-514 Yorodumi Papers
Human CTP synthase filament structure reveals the active enzyme conformation.
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

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


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

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

-
Components

#1: Polypeptide(L)
CTP synthase 1 / CTP synthetase 1 / UTP--ammonia ligase 1


Mass: 66777.297 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P17812, EC: 6.3.4.2

Cellular component

Molecular function

Biological process

#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / UTP *YM


Mass: 484.141 Da / Num. of mol.: 4 / Formula: C9H15N2O15P3

-
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
IDNameCategoryImage processing ID
13SPIDERRECONSTRUCTION1
14hsearch_lorentzRECONSTRUCTION1
15ctffindRECONSTRUCTION1
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

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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)

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 / Changes in new EM Navigator and Yorodumi

Read more