[English] 日本語
Yorodumi
- EMDB-16357: CryoEM structure of Aspergillus nidulans UTP-glucose-1-phosphate ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16357
TitleCryoEM structure of Aspergillus nidulans UTP-glucose-1-phosphate uridylyltransferase
Map dataMain sharpened cryoEM map with D4 symmetry
Sample
  • Complex: UTP--glucose-1-phosphate uridylyltransferase
    • Protein or peptide: UTP--glucose-1-phosphate uridylyltransferase
KeywordsNDP-sugar pyrophosphorylases / UDP-Glc pyrophosphorylases / cell wall biosynthesis / Aspergillus nidulans. / SUGAR BINDING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsHan X / D Angelo C / Otamendi A / Cifuente JO / de Astigarraga E / Ochoa-Lizarralde B / Grininger M / Routier FH / Guerin ME / Fuehring J ...Han X / D Angelo C / Otamendi A / Cifuente JO / de Astigarraga E / Ochoa-Lizarralde B / Grininger M / Routier FH / Guerin ME / Fuehring J / Etxebeste O / Connell SR
Funding support Spain, 1 items
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 JO / de Astigarraga E / Ochoa-Lizarralde B / Grininger M / Routier FH / Guerin ME / Fuehring J / Etxebeste O / Connell SR
History
DepositionDec 16, 2022-
Header (metadata) releaseJun 28, 2023-
Map releaseJun 28, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16357.png

Downloads & links

-
Map

FileDownload / File: emd_16357.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain sharpened cryoEM map with D4 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å		1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.0019824065 - 2.0646195
Average (Standard dev.)0.003472778 (±0.041061617)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Main unsharpened cryoEM map with D4 symmetry

Fileemd_16357_additional_1.map
AnnotationMain unsharpened cryoEM map with D4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened cryoEM map with C1 symmetry

Fileemd_16357_additional_2.map
Annotationunsharpened cryoEM map with C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened cryoEM map with C1 symmetry

Fileemd_16357_additional_3.map
Annotationsharpened cryoEM map with C1 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened locally refined cryoEM map

Fileemd_16357_additional_4.map
Annotationunsharpened locally refined cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened locally refined cryoEM map

Fileemd_16357_additional_5.map
Annotationsharpened locally refined cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Main cryoEM half map A with D4 symmetry

Fileemd_16357_half_map_1.map
AnnotationMain cryoEM half map A with D4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Main cryoEM half map B with D4 symmetry

Fileemd_16357_half_map_2.map
AnnotationMain cryoEM half map B with D4 symmetry
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : UTP--glucose-1-phosphate uridylyltransferase

EntireName: UTP--glucose-1-phosphate uridylyltransferase
Components
  • Complex: UTP--glucose-1-phosphate uridylyltransferase
    • Protein or peptide: UTP--glucose-1-phosphate uridylyltransferase

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

SupramoleculeName: UTP--glucose-1-phosphate uridylyltransferase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aspergillus nidulans FGSC A4 (mold)

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

MacromoleculeName: UTP--glucose-1-phosphate uridylyltransferase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: UTP-glucose-1-phosphate uridylyltransferase
Source (natural)Organism: Aspergillus nidulans FGSC A4 (mold)
Molecular weightTheoretical: 57.634672 KDa
SequenceString: MATKDLPTHL SSNTGFGKHH GKTQSHMAFE NASTSVAASQ MRNALNALAE TVPDPNERKR FEAEMDNFFA LFRRFLNDKA KGNVVNWDR IAPPQPSQVV NYDDIGKESS VEFLNKLAVV KLNGGLGTSM GCVGPKSVIE VREGMSFLDL SVRQIEHLNR T YNVNVPFV ...String:
MATKDLPTHL SSNTGFGKHH GKTQSHMAFE NASTSVAASQ MRNALNALAE TVPDPNERKR FEAEMDNFFA LFRRFLNDKA KGNVVNWDR IAPPQPSQVV NYDDIGKESS VEFLNKLAVV KLNGGLGTSM GCVGPKSVIE VREGMSFLDL SVRQIEHLNR T YNVNVPFV LMNSFNTDQD TQSIIKKYQG HNVDIITFNQ SRYPRIIKDS LLPAPKSFDA PLQDWYPPGH GDVFESLYNS GT LDKLLER GVEYIFLSNA DNLGAVVDTR ILQHMIDTKA EYIMELTDKT KADVKGGTII DYEGKVRLLE IAQVPKEHVN EFK SIKKFK YFNTNNIWMN LRAIKRVVEE NELEMEIIAN EKSIPADKKG EADQAIYQLE TAVGAAIRHF KNAHGVNVPR RRFL PVKTC SDLLLVKSDL YRLEHGQLVM DPNRFGGVPV IKLGSDFKKV SDFQKRIPSI PRIVELDHLT ITGAVNLGRN VTLKG TVII VATEGSTIDI PPGSVLENCV VQGSLRILEH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.18 mg/mL
BufferpH: 7.8
Component:
ConcentrationNameFormula
50.0 mMTris
200.0 mMsodium chlorideNaClSodium chloride
2.0 mMbeta-mercaptoethanol2-Mercaptoethanol

Details: 50 mM Tris, 200 mM NaCl, 2 mM Beta-mercaptoethanol, pH 7.8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126375
FSC plot (resolution estimation)

+
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