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- PDB-7zll: Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 7zll
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 / alpha-D-mannopyranose / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.649 Å
AuthorsRoversi, P. / Zitzmann, N. / Bayo, Y. / Kantsadi, A.L. / Chandran, A.V.
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: Iscience / Year: 2023
Title: A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein folding quality control checkpoint.
Authors: Guay, K.P. / Ibba, R. / Kiappes, J.L. / Vasiljevic, S. / Boni, F. / De Benedictis, M. / Zeni, I. / Le Cornu, J.D. / Hensen, M. / Chandran, A.V. / Kantsadi, A.L. / Caputo, A.T. / Blanco ...Authors: Guay, K.P. / Ibba, R. / Kiappes, J.L. / Vasiljevic, S. / Boni, F. / De Benedictis, M. / Zeni, I. / Le Cornu, J.D. / Hensen, M. / Chandran, A.V. / Kantsadi, A.L. / Caputo, A.T. / Blanco Capurro, J.I. / Bayo, Y. / Hill, J.C. / Hudson, K. / Lia, A. / Brun, J. / Withers, S.G. / Marti, M. / Biasini, E. / Santino, A. / De Rosa, M. / Milani, M. / Modenutti, C.P. / Hebert, D.N. / Zitzmann, N. / Roversi, P.
History
DepositionApr 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 25, 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.title / _citation_author.name
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,7567
Polymers35,4871
Non-polymers1,2686
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-16 kcal/mol
Surface area12980 Å2
Unit cell
Length a, b, c (Å)118.858, 118.858, 68.551
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

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


Mass: 35487.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalytic domain only / Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58
#2: 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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06M Divalents, 0.1 M Buffer System 1, 30% v/v Precipitant Mix 1 (Morpheus screen condition 1-1), 10 mM 5-[(morpholin-4-yl)methyl]quinolin-8-ol in DMSO

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: N2 cryostat / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.649→41.158 Å / Num. obs: 38495 / % possible obs: 88.4 % / Redundancy: 10.5 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.015 / Rrim(I) all: 0.048 / Net I/σ(I): 20.8
Reflection shellResolution: 1.649→1.744 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.596 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1925 / CC1/2: 0.581 / Rpim(I) all: 0.507 / Rrim(I) all: 1.665 / % possible all: 28.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSVERSION Jan 10, 2022data reduction
Aimless0.7.7data scaling
MOLREP11.7.03phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSN

6fsn


Resolution: 1.649→29.71 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.113 / SU Rfree Blow DPI: 0.107 / SU Rfree Cruickshank DPI: 0.107
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 1836 -RANDOM
Rwork0.2091 ---
obs0.2103 38491 88.5 %-
Displacement parametersBiso mean: 39.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.0981 Å20 Å20 Å2
2---0.0981 Å20 Å2
3---0.1962 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.649→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 36 226 2618
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082608HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933586HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d917SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes485HARMONIC5
X-RAY DIFFRACTIONt_it2576HARMONIC10
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2347SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion16.77
LS refinement shellResolution: 1.65→1.72 Å
RfactorNum. reflection% reflection
Rfree0.3009 49 -
Rwork0.3096 --
obs0.309 770 16.15 %

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