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- PDB-6trt: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) d... -

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Basic information

Entry
Database: PDB / ID: 6trt
TitleChaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) double cysteine mutant S180C/T742C.
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsPROTEIN BINDING / Endoplasmic Reticulum / Glycoprotein Folding / ERQC / UGGT / Terbium
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein glycosylation / endoplasmic reticulum lumen / 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
TERBIUM(III) ION / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.58 Å
AuthorsRoversi, P. / Zitzmann, N. / Ibba, R. / Hensen, M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust204801/Z/16/Z United Kingdom
Wellcome Trust106272/Z/14/Z United Kingdom
Wellcome Trust214090/Z/18/Z United Kingdom
Citation
Journal: Structure / Year: 2021
Title: Clamping, bending, and twisting inter-domain motions in the misfold-recognizing portion of UDP-glucose: Glycoprotein glucosyltransferase.
Authors: Modenutti, C.P. / Blanco Capurro, J.I. / Ibba, R. / Alonzi, D.S. / Song, M.N. / Vasiljevic, S. / Kumar, A. / Chandran, A.V. / Tax, G. / Marti, L. / Hill, J.C. / Lia, A. / Hensen, M. / ...Authors: Modenutti, C.P. / Blanco Capurro, J.I. / Ibba, R. / Alonzi, D.S. / Song, M.N. / Vasiljevic, S. / Kumar, A. / Chandran, A.V. / Tax, G. / Marti, L. / Hill, J.C. / Lia, A. / Hensen, M. / Waksman, T. / Rushton, J. / Rubichi, S. / Santino, A. / Marti, M.A. / Zitzmann, N. / Roversi, P.
#1: Journal: Biorxiv / Year: 2019
Title: Clamping, bending, and twisting inter-domain motions in the misfold-recognising portion of UDP-glucose:glycoprotein glucosyl-transferase
Authors: Roversi, P. / Zitzmann, N.
History
DepositionDec 19, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine_hist / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine_hist.d_res_high / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 13, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / struct_conn
Item: _chem_comp.pdbx_synonyms / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Apr 14, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.title / _citation.year
Revision 2.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)173,1469
Polymers169,6561
Non-polymers3,4908
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint26 kcal/mol
Surface area62870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.799, 148.799, 235.546
Angle α, β, γ (deg.)90, 90, 120
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1441-

MET

21A-1441-

MET

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Components

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


Mass: 169656.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Gene: CTHT_0048990 / Plasmid: pHLsec / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-TB / TERBIUM(III) ION


Mass: 158.925 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Tb
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
Has ligand of interestN

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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: 4.44 Å3/Da / Density % sol: 72.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2 mM Lanthanides (0.005M Yttrium(III) chloride hexahydrate, 0.005M Erbium(III) chloride hexahydrate, 0.005M Terbium(III) chloride hexahydrate, 0.005M Ytterbium(III) chloride hexahydrate), 0. ...Details: 2 mM Lanthanides (0.005M Yttrium(III) chloride hexahydrate, 0.005M Erbium(III) chloride hexahydrate, 0.005M Terbium(III) chloride hexahydrate, 0.005M Ytterbium(III) chloride hexahydrate), 0.1 M Buffer System 6 (Gly-Gly, AMPD pH 8.5), 36 % v/v Precipitant Mix 5 (30% w/v PEG 3000, 40% v/v 1, 2, 4- Butanetriol, 2% w/v NDSB 256

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 4.58→128.864 Å / Num. obs: 9520 / % possible obs: 90.1 % / Redundancy: 8.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.042 / Rrim(I) all: 0.125 / Net I/σ(I): 10.6
Reflection shellResolution: 4.58→5.13 Å / Rmerge(I) obs: 1.563 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 476 / CC1/2: 0.411 / Rpim(I) all: 0.523 / Rrim(I) all: 1.65

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nv4

5nv4


Resolution: 4.58→128.86 Å / Cor.coef. Fo:Fc: 0.753 / Cor.coef. Fo:Fc free: 0.758 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 1.726
RfactorNum. reflection% reflectionSelection details
Rfree0.2968 418 -RANDOM
Rwork0.2909 ---
obs0.2911 9520 54.9 %-
Displacement parametersBiso mean: 142.96 Å2
Baniso -1Baniso -2Baniso -3
1--8.3046 Å20 Å20 Å2
2---8.3046 Å20 Å2
3---16.6092 Å2
Refine analyzeLuzzati coordinate error obs: 0.99 Å
Refinement stepCycle: LAST / Resolution: 4.58→128.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11007 0 203 0 11210
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00611500HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9915617HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4049SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1928HARMONIC5
X-RAY DIFFRACTIONt_it11276HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1508SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7738SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion17.28
LS refinement shellResolution: 4.555→5.12 Å
RfactorNum. reflection% reflection
Rfree0.2555 25 -
Rwork0.2517 --
obs--9.36 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.47240.32271.26837.821-2.62844.2435-0.16810.23750.69870.23750.022-0.15540.6987-0.15540.1460.2699-0.00060.2031-0.0804-0.04790.2117-34.5884-86.441214.3987
28.6381-1.0151.97284.41882.40384.80050.2343-0.19950.1992-0.1995-0.58340.74350.19920.74350.34910.28360.1872-0.2076-0.28360.05560.0753-42.9144-23.79622.1502
33.63070.7547-2.42723.4196-1.61688.31550.21660.7216-0.07560.7216-0.12290.5592-0.07560.5592-0.0937-0.01760.05810.1272-0.33240.0836-0.1667-57.3565-62.202720.9419
44.5991-2.6550.33426.4885-1.83785.7549-0.1175-0.44250.5101-0.4425-0.235-0.25770.5101-0.25770.3525-0.21210.11290.20760.0084-0.0556-0.2219-45.0841-66.3505-20.047
57.0902-1.08963.25887.46570.17648.3155-0.37260.03380.67470.0338-0.1095-0.1590.6747-0.1590.48210.10540.29020.1934-0.1054-0.0310.304-22.3753-79.3332-19.4554
63.68490.5748-1.16997.8397-3.79450-0.11810.6606-0.64050.6606-0.33110.2586-0.64050.25860.44910.02040.33920.0556-0.02040.20760.1092-21.7684-57.37848.8666
78.9326-1.59-3.05274.0473-0.53344.61680.09770.11220.1630.11220.4150.72260.1630.7226-0.5128-0.10790.26520.2076-0.0631-0.05560.304-1.5386-57.2591-16.4219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|45 - A|224 A|2056 - A|2064 }
2X-RAY DIFFRACTION2{ A|414 - A|666 A|1638 - A|1640}
3X-RAY DIFFRACTION3{ A|667 - A|871 A|9001 A|9002}
4X-RAY DIFFRACTION4{ A|243 - A|413 A|872 - A|950 A|2329 A|1894}
5X-RAY DIFFRACTION5{ A|28 - A|44 A|225 - A|242 A|951 - A|1037 }
6X-RAY DIFFRACTION6{ A|1038 - A|1152 }
7X-RAY DIFFRACTION7{ A|1194 - A|1473 A|9000 A|2227 - A|2229 }

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