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- PDB-5mu1: UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium ther... -

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Basic information

Entry
Database: PDB / ID: 5mu1
TitleUDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum soaked with K2PtI6
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum
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
IODIDE ION / : / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.48 Å
AuthorsRoversi, P. / Caputo, A.T. / Hill, J. / Alonzi, D.S. / Zitzmann, N.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust097300/Z/11/Z United Kingdom
Wellcome Trust106272/Z/14/Z United Kingdom
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interdomain conformational flexibility underpins the activity of UGGT, the eukaryotic glycoprotein secretion checkpoint.
Authors: Roversi, P. / Marti, L. / Caputo, A.T. / Alonzi, D.S. / Hill, J.C. / Dent, K.C. / Kumar, A. / Levasseur, M.D. / Lia, A. / Waksman, T. / Basu, S. / Soto Albrecht, Y. / Qian, K. / McIvor, J.P. ...Authors: Roversi, P. / Marti, L. / Caputo, A.T. / Alonzi, D.S. / Hill, J.C. / Dent, K.C. / Kumar, A. / Levasseur, M.D. / Lia, A. / Waksman, T. / Basu, S. / Soto Albrecht, Y. / Qian, K. / McIvor, J.P. / Lipp, C.B. / Siliqi, D. / Vasiljevic, S. / Mohammed, S. / Lukacik, P. / Walsh, M.A. / Santino, A. / Zitzmann, N.
History
DepositionJan 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 8, 2020Group: Data collection / Category: chem_comp / diffrn_detector
Item: _chem_comp.type / _diffrn_detector.pdbx_collection_date
Revision 1.4Jun 3, 2020Group: Derived calculations
Category: struct_conn / struct_sheet ...struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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.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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_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 2.1Mar 8, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _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)176,91726
Polymers169,6381
Non-polymers7,27925
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7240 Å2
ΔGint-119 kcal/mol
Surface area64850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.950, 116.950, 301.491
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 169638.328 Da / Num. of mol.: 1 / Fragment: UNP Residues 24-1505
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0048990 / Plasmid: pHLSec / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58

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Sugars , 4 types, 4 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3[DManpa1-6DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d3-e1_f6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_d6-e1WURCSPDB2Glycan 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]{}}}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_d6-e1_e3-f1_e6-g1WURCSPDB2Glycan 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]{}[(6+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 21 molecules

#6: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Formula: I
#7: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pt
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Ca

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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: 3.83 Å3/Da / Density % sol: 67.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 51.4 mM MES pH 3.3, 44.6 Imidazole pH 8.3, 20% PEG 8K, 10% Ethylene Glycole, 120 mM Morpheus Ethylene glycols mix

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.07141 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Nov 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07141 Å / Relative weight: 1
ReflectionResolution: 3.48→150.75 Å / Num. obs: 28757 / % possible obs: 96.2 % / Redundancy: 23.2 % / Biso Wilson estimate: 125.58 Å2 / Net I/σ(I): 15.4
Reflection shellResolution: 3.48→3.67 Å / Redundancy: 23.3 % / Rmerge(I) obs: 3.573 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4354 / Num. unique obs: 4354 / CC1/2: 0.482 / Rpim(I) all: 1.089 / Rrim(I) all: 3.73 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3.48→101.28 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.578
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1269 4.9 %RANDOM
Rwork0.237 ---
obs0.238 25903 86.8 %-
Displacement parametersBiso mean: 151.75 Å2
Baniso -1Baniso -2Baniso -3
1-1.7215 Å20 Å20 Å2
2--1.7215 Å20 Å2
3----3.443 Å2
Refine analyzeLuzzati coordinate error obs: 0.57 Å
Refinement stepCycle: 1 / Resolution: 3.48→101.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11066 0 309 0 11375
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112024HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.2416669HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4153SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes291HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1700HARMONIC5
X-RAY DIFFRACTIONt_it12024HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.24
X-RAY DIFFRACTIONt_other_torsion18.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1558SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact13651SEMIHARMONIC4
LS refinement shellResolution: 3.48→3.62 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2706 -5.44 %
Rwork0.23 1200 -
all0.2323 1269 -
obs--37.88 %
Refinement TLS params.

Method: refined / 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)
12.2116-0.16590.62656.6645-2.10960.9370.04720.21690.7351-0.4281-0.0103-0.204-0.38920.0897-0.0369-0.1731-0.251-0.19890.17310.0606-0.255816.938564.64111.401
21.95061.8367-0.61864.47213.00352.23970.2501-0.0154-0.4592-0.053-0.216-0.2885-0.40310.0897-0.0341-0.0204-0.33920.0220.0204-0.1628-0.3042.821854.8261177.244
31.71391.34931.52216.87713.18445.38890.40710.04240.1016-0.1198-0.5074-0.5698-0.44930.32530.1003-0.2959-0.0986-0.04980.0180.0265-0.240226.44362.4389145.903
44.04720.9081.02263.31740.31292.8801-0.07040.1085-0.59280.30460.07670.24920.18040.2582-0.0063-0.20030.0287-0.09920.09280.0057-0.099211.981626.4813127.194
53.77020.11091.50126.0890.28965.067-0.23770.6273-0.4446-0.2413-0.20670.35710.34650.22820.4443-0.2993-0.16-0.15250.2364-0.0398-0.304-3.147733.2133105.953
62.3188-0.31061.37121.58141.42271.2253-0.0516-0.31880.41610.27680.11860.3678-0.30640.2091-0.067-0.02790.1804-0.20320.11480.04790.1431-7.657260.0016130.868
76.67080.24821.11641.3349-0.12654.1541-0.58690.30650.27240.30770.21360.5192-0.0314-0.30580.3733-0.27030.0281-0.16320.04830.0812-0.0576-30.208842.1405116.122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|39 - A|225 A|2056 - A|2060}
2X-RAY DIFFRACTION2{ A|414 - A|666 A|1638 - A|1644 A|1614 A|1621 A|1625 A|1629 }
3X-RAY DIFFRACTION3{ A|667 - A|880 }
4X-RAY DIFFRACTION4{ A|279 - A|413 A|881 - A|950 A|2329 - A|2334 A|1894 - A|1898 }
5X-RAY DIFFRACTION5{ A|27 - A|38 A|226 - A|245 A|951 - A|1037 }
6X-RAY DIFFRACTION6{ A|1038 - A|1152 }
7X-RAY DIFFRACTION7{ A|1191 - A|1474 A|2227 - A|2233 A|1633 A|1617 A|9000 }

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