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- PDB-6fsn: Catalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 6fsn
TitleCatalytic domain of UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum in complex with UDP-glucose (conformation 1)
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 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
TRIETHYLENE GLYCOL / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsRoversi, P. / Le Cornu, J.D. / Hill, J. / Alonzi, D.S. / Zitzmann, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust106272/Z/14/Z United Kingdom
CitationJournal: Front Mol Biosci / Year: 2022
Title: Crystal polymorphism in fragment-based lead discovery of ligands of the catalytic domain of UGGT, the glycoprotein folding quality control checkpoint.
Authors: Caputo, A.T. / Ibba, R. / Le Cornu, J.D. / Darlot, B. / Hensen, M. / Lipp, C.B. / Marciano, G. / Vasiljevic, S. / Zitzmann, N. / Roversi, P.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2020Group: Data collection / Category: chem_comp / Item: _chem_comp.type
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _software.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 30, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 21, 2022Group: Database references / Category: citation / Item: _citation.year
Revision 1.5Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5276
Polymers35,4871
Non-polymers1,0405
Water4,540252
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration, Monomeric globular.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-12 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.832, 118.832, 68.754
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0048990 / Plasmid: pHLsec / 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.: 1
Source method: isolated from a genetically manipulated source
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, 256 molecules

#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: 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
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 53.11 % / Description: Chunky prisms
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.12 M Morpheus Screen Ethylene glycols 0.1 M Morpheus Screen Buffer System 3 pH 8.5 50% v/v Morpheus Screen Precipitant Mix

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Data collection

DiffractionMean temperature: 120 K / Ambient temp details: Cryostat
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 pair for horizontal and vertical focussing
RadiationMonochromator: double crystal. Crystal Type, Si(111) / 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: 94855 / % possible obs: 99 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.53 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.035 / Rrim(I) all: 0.081 / 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: 13700 / CC1/2: 0.502 / Rpim(I) all: 0.689 / Rrim(I) all: 1.56 / % possible all: 97.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSJun 1, 2017data reduction
autoPROC1.0.5data scaling
MOLREP11.5.04phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nv4

5nv4


Resolution: 1.19→13.77 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.053 / SU Rfree Cruickshank DPI: 0.053 / Details: autoBUSTER 2.10.3
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4421 5.08 %RANDOM
Rwork0.211 ---
obs0.211 87031 75.4 %-
Displacement parametersBiso mean: 26.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.1062 Å20 Å20 Å2
2--0.1062 Å20 Å2
3----0.2123 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: 1 / Resolution: 1.19→13.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 65 252 2643
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014984HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.068977HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1103SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes798HARMONIC5
X-RAY DIFFRACTIONt_it4984HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.34
X-RAY DIFFRACTIONt_other_torsion14.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance1HARMONIC1
X-RAY DIFFRACTIONt_utility_angle2HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5644SEMIHARMONIC4
LS refinement shellResolution: 1.19→1.22 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 -5.83 %
Rwork0.2369 113 -
all0.2373 120 -
obs--1.33 %

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