[English] 日本語
Yorodumi
- PDB-8c0b: CryoEM structure of Aspergillus nidulans UTP-glucose-1-phosphate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8c0b
TitleCryoEM structure of Aspergillus nidulans UTP-glucose-1-phosphate uridylyltransferase
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsSUGAR BINDING PROTEIN / NDP-sugar pyrophosphorylases / UDP-Glc pyrophosphorylases / cell wall biosynthesis / Aspergillus nidulans.
Function / homology
Function and homology information


(1->6)-beta-D-glucan biosynthetic process / sporulation / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / trehalose biosynthetic process / anatomical structure development / glycogen biosynthetic process / glycogen metabolic process / cell differentiation / cytoplasm
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsHan, X. / D Angelo, C. / Otamendi, A. / Cifuente, J.O. / de Astigarraga, E. / Ochoa-Lizarralde, B. / Grininger, M. / Routier, F.H. / Guerin, M.E. / Fuehring, J. ...Han, X. / D Angelo, C. / Otamendi, A. / Cifuente, J.O. / de Astigarraga, E. / Ochoa-Lizarralde, B. / Grininger, M. / Routier, F.H. / Guerin, M.E. / Fuehring, J. / Etxebeste, O. / Connell, S.R.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2021-122705OB-I00 Spain
CitationJournal: To Be Published
Title: Molecular mechanism of UDP-Glc biosynthesis by the essential UDP-Glc pyrophosphorylase from Aspergillus nidulans
Authors: Han, X. / D Angelo, C. / Otamendi, A. / Cifuente, J.O. / de Astigarraga, E. / Ochoa-Lizarralde, B. / Grininger, M. / Routier, F.H. / Guerin, M.E. / Fuehring, J. / Etxebeste, O. / Connell, S.R.
History
DepositionDec 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase
E: UTP--glucose-1-phosphate uridylyltransferase
F: UTP--glucose-1-phosphate uridylyltransferase
G: UTP--glucose-1-phosphate uridylyltransferase
H: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)461,0778
Polymers461,0778
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

#1: Protein
UTP--glucose-1-phosphate uridylyltransferase


Mass: 57634.672 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Aspergillus nidulans FGSC A4 (mold)
References: UniProt: C8VK50, UTP-glucose-1-phosphate uridylyltransferase

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: UTP--glucose-1-phosphate uridylyltransferase / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Aspergillus nidulans FGSC A4 (mold)
Buffer solutionpH: 7.8
Details: 50 mM Tris, 200 mM NaCl, 2 mM Beta-mercaptoethanol, pH 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2200 mMsodium chlorideNaClSodium chloride1
32 mMbeta-mercaptoethanol2-Mercaptoethanol1
SpecimenConc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was monodisperse
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4788refinement
PHENIXdev_4788refinement
UCSF ChimeraX1.5/v9model building
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126375 / Symmetry type: POINT

+
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