[English] 日本語
Yorodumi
- PDB-7zxw: Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zxw
TitleCatalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with the 5-[(morpholin-4-yl)methyl]quinolin-8-ol inhibitor
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum / GT24 / 5-[(morpholin-4-yl)methyl]quinolin-8-ol
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / unfolded protein binding / endoplasmic reticulum lumen / nucleotide binding / metal ion binding
Similarity search - Function
UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain ...UDP-glucose:glycoprotein glucosyltransferase, thioredoxin-like domain 4 / UGGT, thioredoxin-like domain 3 / UGGT, thioredoxin-like domain 1 / UGGT, thioredoxin-like domain 2 / UDP-glucose:Glycoprotein Glucosyltransferase / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Thioredoxin-like domain / Glucosyltransferase 24, catalytic domain / Glucosyltransferase 24 / UDP-glucose:Glycoprotein Glucosyltransferase / Nucleotide-diphospho-sugar transferases / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
5-(morpholin-4-ylmethyl)quinolin-8-ol / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesThermochaetoides thermophila DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.246 Å
AuthorsLe Cornu, J.D. / Ibba, R. / Roversi, P. / Zitzmann, N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust106272/Z/14/Z United Kingdom
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
CitationJournal: Front Mol Biosci / Year: 2022
Title: Crystal polymorphism in fragment-based lead discovery of ligands of the catalytic domain of UGGT, the glycoprotein folding quality control checkpoint.
Authors: Caputo, A.T. / Ibba, R. / Le Cornu, J.D. / Darlot, B. / Hensen, M. / Lipp, C.B. / Marciano, G. / Vasiljevic, S. / Zitzmann, N. / Roversi, P.
History
DepositionMay 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation_author
Item: _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,88510
Polymers35,0571
Non-polymers1,8289
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2320 Å2
ΔGint-4 kcal/mol
Surface area13180 Å2
Unit cell
Length a, b, c (Å)118.009, 118.009, 68.373
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein UDP-glucose-glycoprotein glucosyltransferase-like protein


Mass: 35056.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: G0SB58
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 202 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-JM3 / 5-(morpholin-4-ylmethyl)quinolin-8-ol


Mass: 244.289 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N2O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.14 % / Description: Chunky polyhedra
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.6% v/v PEG 500 MME; 10.3 % w/v PEG 20000, Tris-Bicine 0.1 M pH 8.5
PH range: 8.4-8.6 / Temp details: N2 Cryo-stream

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.246→59.27 Å / Num. obs: 16926 / % possible obs: 92.6 % / Redundancy: 1.8 % / CC1/2: 0.97 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.16 / Rrim(I) all: 0.226 / Net I/σ(I): 2.4
Reflection shellResolution: 2.246→2.67 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2464 / CC1/2: 0.423 / Rpim(I) all: 0.51 / Rrim(I) all: 1.14 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6FSN

6fsn


Resolution: 2.246→59.01 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.928 / SU R Cruickshank DPI: 0.302 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.307 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.215
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 965 -RANDOM
Rwork0.2025 ---
obs0.2048 16926 99.9 %-
Displacement parametersBiso mean: 36.16 Å2
Baniso -1Baniso -2Baniso -3
1--2.7747 Å20 Å20 Å2
2---2.7747 Å20 Å2
3---5.5494 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 2.246→59.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 114 194 2679
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082592HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.953527HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d907SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes459HARMONIC5
X-RAY DIFFRACTIONt_it2592HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion326SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2393SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion16.25
LS refinement shellResolution: 2.25→2.26 Å
RfactorNum. reflection% reflection
Rfree0.2933 24 -
Rwork0.3258 --
obs0.3235 353 99.7 %

+
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://pdbjlvh1.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