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

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Basic information

Entry
Database: PDB / ID: 7zle
TitleCatalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum. UDP / 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 / URIDINE-5'-DIPHOSPHATE / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.823 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 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 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
Revision 1.3Oct 16, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,4298
Polymers35,4871
Non-polymers9427
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-2 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.586, 119.586, 67.234
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: 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
#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.: 1 / 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 , 5 types, 156 molecules

#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#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-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.61 Å3/Da / Density % sol: 52.82 % / Description: Chunky polyhedron
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.12 M Alcohols, 0.1 M Buffer System 2 pH 7.5, 37.5% v/v Precipitant Mix 1 (Morpheus condition 1-41)

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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: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2017
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.823→56.39 Å / Num. obs: 29832 / % possible obs: 99.4 % / Redundancy: 8.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.066 / Rrim(I) all: 0.211 / Net I/σ(I): 10.7
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 1.248 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3816 / CC1/2: 0.514 / Rpim(I) all: 0.619 / Rrim(I) all: 1.395 / % possible all: 87.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6FSN

6fsn


Resolution: 1.823→22.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.125 / Details: External restraints to 6FSN
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1533 -RANDOM
Rwork0.2113 ---
obs0.2122 29832 93.2 %-
Displacement parametersBiso mean: 44.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.2028 Å20 Å20 Å2
2--0.2028 Å20 Å2
3----0.4055 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 1.823→22.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2375 0 60 148 2583
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092588HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.913501HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d914SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes441HARMONIC5
X-RAY DIFFRACTIONt_it2585HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion319SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance2HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2162SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion15.18
LS refinement shellResolution: 1.823→1.87 Å
RfactorNum. reflection% reflection
Rfree0.3304 26 -
Rwork0.3381 --
obs--26.93 %

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