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- PDB-6trf: Chaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) p... -

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Basic information

Entry
Database: PDB / ID: 6trf
TitleChaetomium thermophilum UDP-Glucose Glucosyl Transferase (UGGT) purified from cells treated with kifunensine.
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsPROTEIN BINDING / Endoplasmic Reticulum / Glycoprotein Folding / ERQC / kifunensine / UGGT
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 / Nucleotide-diphospho-sugar transferases / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.106 Å
AuthorsRoversi, P. / Zitzmann, N.
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 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / 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 / pdbx_unobs_or_zero_occ_atoms / 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.occupancy / _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.id / _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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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
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
Revision 2.4Nov 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

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)171,1945
Polymers169,6381
Non-polymers1,5554
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint23 kcal/mol
Surface area63510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.655, 148.928, 190.298
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 169638.328 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 line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#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.: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN
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: 3.29 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.03M Sodium nitrate, 0.03 Sodium phosphate dibasic, 0.03M Ammonium sulfate; Tris Bicine pH 8.5; 40% v/v Glycerol, 20% w/v PEG 4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.106→95.149 Å / Num. obs: 7500 / % possible obs: 90.2 % / Redundancy: 10.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.047 / Rrim(I) all: 0.157 / Net I/σ(I): 9.9
Reflection shellResolution: 4.106→4.493 Å / Redundancy: 15.9 % / Rmerge(I) obs: 3.268 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 271 / CC1/2: 0.566 / Rpim(I) all: 0.836 / Rrim(I) all: 3.376 / % possible all: 72.4

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Processing

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

5nv4


Resolution: 4.106→95.149 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.824 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 2.033
Details: The structure was refined in autoBUSTER with one TLS body per domain, one rigid body per domain, with external restraints to PDB ID 5NV4.
RfactorNum. reflection% reflectionSelection details
Rfree0.3154 351 -RANDOM
Rwork0.2551 ---
obs0.2577 7500 40.7 %-
Displacement parametersBiso mean: 270.25 Å2
Baniso -1Baniso -2Baniso -3
1-26.1611 Å20 Å20 Å2
2---63.1082 Å20 Å2
3---36.947 Å2
Refine analyzeLuzzati coordinate error obs: 0.9 Å
Refinement stepCycle: LAST / Resolution: 4.106→95.149 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10616 0 101 0 10717
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00610989HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9514897HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3854SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1850HARMONIC5
X-RAY DIFFRACTIONt_it10873HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1416SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact7142SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion19.8
LS refinement shellResolution: 4.082→4.62 Å
RfactorNum. reflection% reflection
Rfree0.2157 19 -
Rwork0.2564 --
obs--7.89 %
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)
18.3155-0.2771-2.91046.5802-2.91048.31550.20280.41330.36720.4133-0.3414-0.54420.3672-0.54420.1386-0.3040.152-0.10850.304-0.152-0.2417-8.8398-0.4676-9.4661
28.3155-2.9104-2.7698.31542.04938.31550.26790.54420.54420.54420.0084-0.27480.5442-0.2748-0.2763-0.3040.1520.1520.3040.1520.30440.1708-11.832830.5961
38.3155-2.9104-2.04791.1446-1.23571.0034-0.3511-0.3352-0.5442-0.33520.1932-0.2525-0.5442-0.25250.1579-0.09510.1520.11740.1009-0.1345-0.122210.392713.964124.8952
48.31550.5108-2.91046.4719-1.91031.84610-0.5442-0.5442-0.54420.54420.5442-0.54420.5442-0.54420.1864-0.1520.1109-0.304-0.0145-0.104530.185414.3265-16.3149
55.6283-0.23381.43792.31122.55890.63390.0061-0.5263-0.5442-0.5263-0.5382-0.5442-0.5442-0.54420.5321-0.14830.152-0.13030.140.1092-0.30419.0996-2.0833-32.8005
68.31552.9104-2.91044.8295-2.91045.05310.03340.54420.51850.5442-0.51090.32040.51850.32040.4775-0.04460.1520.152-0.30390.152-0.05514.7843-21.1737-2.4703
70-2.49510.69788.31542.91048.31550-0.54420.5442-0.54420.5442-0.00760.5442-0.0076-0.54420.3040.152-0.1365-0.15690.10450.107430.6795-29.7155-29.1039
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|45 - A|224 A|1802 - A|1807 }
2X-RAY DIFFRACTION2{ A|414 - A|666 }
3X-RAY DIFFRACTION3{ A|667 - A|871 }
4X-RAY DIFFRACTION4{ A|243 - A|413 A|887 - A|950 }
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|1193 - A|1476 A|1606 A|1801 }

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