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

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Basic information

Entry
Database: PDB / ID: 7zhb
TitleCatalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-glucose (conformation 2)
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum. UDP-glucose / GT24
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
ISOPROPYL ALCOHOL / 1,3-PROPANDIOL / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsRoversi, P. / Zitzmann, N. / Bayo, Y. / Le Cornu, J.D.
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: To Be Published
Title: A quinolin-8-ol sub-millimolar inhibitor of UGGT, the ER glycoprotein quality control checkpoint
Authors: Caputo, A.T. / Ibba, R. / Le Cornu, J.D. / Darlot, B. / Hensen, M. / Lipp, C.B. / Marciano, G. / Vasiljevic, S. / Roversi, P. / Zitzmann, N.
History
DepositionApr 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Structure summary / Category: audit_author / 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 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)36,92710
Polymers35,4871
Non-polymers1,4399
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint3 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.442, 121.442, 62.117
Angle α, β, γ (deg.)90, 90, 120
Int Tables number146
Space group name H-MH3

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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: ETG (Nterm) and GTKHHHHHH (Cterm) from cloning vector
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Plasmid: pHLsec / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 5 types, 94 molecules

#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C3H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.48 Å3/Da / Density % sol: 50.48 % / Description: Polyhedron
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus condition 1-40 (0.12 M Alcohols, 0.1 M Buffer System 1 pH 482 6.5, 37.5% v/v Precipitant Mix 4)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2017 / Details: Bimorph Kirkpatrick-Baez mirrors, or KB mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.89→60.72 Å / Num. obs: 24990 / % possible obs: 96.7 % / Redundancy: 5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.07 / Net I/σ(I): 11
Reflection shellResolution: 1.89→2.03 Å / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3379 / CC1/2: 0.53 / Rrim(I) all: 1.25

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimless0.5.3data scaling
autoBUSTER2.10.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSN

6fsn


Resolution: 1.89→21.26 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.154 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 1275 -RANDOM
Rwork0.184 ---
obs0.1853 24189 88.5 %-
Displacement parametersBiso mean: 51.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.0169 Å20 Å20 Å2
2--0.0169 Å20 Å2
3----0.0337 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.89→21.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2391 0 92 86 2569
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082708HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.933722HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d970SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes458HARMONIC5
X-RAY DIFFRACTIONt_it2668HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion342SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2189SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion16.39
LS refinement shellResolution: 1.89→1.97 Å
RfactorNum. reflection% reflection
Rfree0.331 29 -
Rwork0.3331 --
obs0.333 484 16 %

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