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

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Basic information

Entry
Database: PDB / ID: 7zkc
TitleCatalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum (apo form)
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 / ERAD pathway / 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 / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.769 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: 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 12, 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 / 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 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 / _citation_author.name
Revision 1.3Oct 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_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Oct 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 1.5Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.6Nov 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)35,9523
Polymers35,4871
Non-polymers4642
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area440 Å2
ΔGint-6 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.825, 118.825, 68.441
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: ETG at the Nterm and GTKHHHHHH are from cloning vector
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Cell (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
DGlcpNAcb1-4DGlcpNAcbGlycam 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
[][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 53.06 % / Description: CHUNKY PRISMS
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)

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Data collection

DiffractionMean temperature: 120 K / Ambient temp details: N2 cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97956 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2017 / Details: KIRKPATRICK BAEZ BIMORPH MIRROR
RadiationMonochromator: DOUBLE CRYSTAL. CRYSTAL TYPE, / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97956 Å / Relative weight: 1
ReflectionResolution: 1.19→57.17 Å / Num. obs: 35287 / % possible obs: 99 % / Redundancy: 5.1 % / CC star: 0.99 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.15 / Net I/σ(I): 10.5
Reflection shellResolution: 1.19→1.34 Å / Redundancy: 5 % / Rmerge(I) obs: 1.397 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5115 / CC star: 0.35 / Rrim(I) all: 2.25 / % possible all: 97.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSJUN 1, 2017data reduction
autoPROC1.0.5data scaling
MOLREP11.5.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NV4

5nv4


Resolution: 1.769→41.13 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.952 / SU R Cruickshank DPI: 0.134 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.121 / SU Rfree Cruickshank DPI: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 1525 -RANDOM
Rwork0.2049 ---
obs0.2061 31424 89.3 %-
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.5167 Å20 Å20 Å2
2---0.5167 Å20 Å2
3---1.0334 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.769→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 29 227 2592
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082519HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.93438HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d895SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes437HARMONIC5
X-RAY DIFFRACTIONt_it2519HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact2251SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion15.72
LS refinement shellResolution: 1.77→1.82 Å
RfactorNum. reflection% reflection
Rfree0.3308 30 -
Rwork0.3169 --
obs0.3174 629 22.22 %
Refinement TLS params.Origin x: -31.623 Å / Origin y: 17.5113 Å / Origin z: 0.2877 Å
111213212223313233
T-0.0884 Å20.0108 Å20.0052 Å2--0.0565 Å2-0.0531 Å2---0.0393 Å2
L1.0475 °20.9312 °20.0936 °2-3.2161 °21.9168 °2--3.6497 °2
S-0.0191 Å °-0.2392 Å °-0.3913 Å °-0.2392 Å °-0.243 Å °-0.3951 Å °-0.3913 Å °-0.3951 Å °0.2621 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1196 - 1473
2X-RAY DIFFRACTION1{ A|* }A4500 - 2228

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