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

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Basic information

Entry
Database: PDB / ID: 7zlu
TitleCatalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-2-deoxy-2-fluoro-D-glucose
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum / UDP-2-deoxy-2-fluoro-D-glucose / GT24
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein glycosylation / 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
1,3-PROPANDIOL / Chem-U2F / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.049 Å
AuthorsRoversi, P. / Zitzmann, N. / Bayo, Y. / Ibba, R.
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 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Category: citation_author
Revision 1.2Oct 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 1.3Oct 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 1.4Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)108,35015
Polymers105,6333
Non-polymers2,71712
Water5,260292
1
A: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1175
Polymers35,2111
Non-polymers9064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1175
Polymers35,2111
Non-polymers9064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-glucose-glycoprotein glucosyltransferase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1175
Polymers35,2111
Non-polymers9064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.159, 72.316, 72.393
Angle α, β, γ (deg.)110.48, 108.33, 108.26
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 6 molecules ABC

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


Mass: 35211.086 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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: 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

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Non-polymers , 4 types, 301 molecules

#3: Chemical ChemComp-U2F / URIDINE-5'-DIPHOSPHATE-2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE


Mass: 568.293 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H23FN2O16P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.44 % / Description: chunky prisms
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Monosaccharides, 0.1 M Buffer System 2 pH 7.5, 30% v/v Precipitant Mix 1, (Morpheus condition 2-17), 1.25 mM U2F

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: nitrogen crystream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97956 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 2.06→41.16 Å / Num. obs: 39166 / % possible obs: 81.1 % / Redundancy: 1.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.054 / Rrim(I) all: 0.076 / Net I/σ(I): 8.4
Reflection shellResolution: 2.06→2.32 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3486 / CC1/2: 0.646 / Rpim(I) all: 0.423 / Rrim(I) all: 0.599 / % possible all: 45.9

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSNov 11, 2017data reduction
Aimless0.6.2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSN

6fsn


Resolution: 2.049→41.16 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.512 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.477 / SU Rfree Blow DPI: 0.283 / SU Rfree Cruickshank DPI: 0.291
RfactorNum. reflection% reflectionSelection details
Rfree0.2701 1863 -RANDOM
Rwork0.226 ---
obs0.228 39188 57.7 %-
Displacement parametersBiso mean: 36.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.3598 Å2-0.2415 Å2-0.024 Å2
2---0.056 Å20.537 Å2
3---1.4159 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.049→41.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7008 0 168 292 7468
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087533HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9410290HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2646SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1289HARMONIC5
X-RAY DIFFRACTIONt_it7501HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion946SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6299SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.27
X-RAY DIFFRACTIONt_other_torsion16.57
LS refinement shellResolution: 2.05→2.22 Å
RfactorNum. reflection% reflection
Rfree0.4448 45 -
Rwork0.3218 --
obs0.3287 784 5.43 %

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