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

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Basic information

Entry
Database: PDB / ID: 5mzo
TitleUDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum (open conformation)
ComponentsUDP-glucose-glycoprotein glucosyltransferase-like protein
KeywordsTRANSFERASE / glycoprotein / misfolding / endoplasmic reticulum
Function / homology
Function and homology information


UDP-glucose:glycoprotein glucosyltransferase activity / protein N-linked glycosylation via asparagine / 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 / 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
DepositionFeb 1, 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 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.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.type / _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 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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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)172,2089
Polymers169,6381
Non-polymers2,5698
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint31 kcal/mol
Surface area62260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.570, 163.570, 248.584
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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
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 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: G0SB58

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Sugars , 3 types, 5 molecules

#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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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
#4: 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 , 3 types, 15 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 24 mM Morpheus alchools mix, 20 mM Morpheus buffer system 3 pH 8.5, 2.5% v/v MPD, 2.5% w/v PEG 1000, 2.5% w/v PEG 3350, 1.6 mM CaCl2 and 50 uM UDP-glucose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91741 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91741 Å / Relative weight: 1
ReflectionResolution: 3.48→124.29 Å / Num. obs: 25652 / % possible obs: 100 % / Redundancy: 11.8 % / Biso Wilson estimate: 103.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.25 / Rpim(I) all: 0.1 / Rsym value: 0.26 / Net I/σ(I): 9.2
Reflection shellResolution: 3.48→3.68 Å / Redundancy: 12.2 % / Rmerge(I) obs: 3.18 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3643 / CC1/2: 0.49 / Rpim(I) all: 1.29 / Rsym value: 3.33 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementStarting model: 5MU1

5mu1


Resolution: 3.48→102 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.638
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1281 5.05 %RANDOM
Rwork0.251 ---
obs0.252 25379 98 %-
Displacement parametersBiso mean: 171.15 Å2
Baniso -1Baniso -2Baniso -3
1--24.2068 Å20 Å20 Å2
2---24.2068 Å20 Å2
3---48.4137 Å2
Refine analyzeLuzzati coordinate error obs: 0.71 Å
Refinement stepCycle: LAST / Resolution: 3.48→102 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11035 0 168 12 11215
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00911497HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2115612HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4043SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes289HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1643HARMONIC5
X-RAY DIFFRACTIONt_it11497HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1493SEMIHARMONIC5
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_contact13077SEMIHARMONIC4
LS refinement shellResolution: 3.48→3.62 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.3062 118 5 %
Rwork0.2529 2241 -
all0.2555 2359 -
obs--82.51 %
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)
12.3571-1.18070.21026.70990.09161.9607-0.0870.1543-0.41860.0447-0.0872-0.0271-0.0806-0.3090.1742-0.1399-0.1962-0.2004-0.11660.05980.1534-6.1814-75.0713-10.2122
23.6324-0.5211-0.28651.3634-2.87884.57310.01890.1669-0.1137-0.05030.11480.15040.320.286-0.13380.06930.17120.05560.22260.2076-0.299117.9996-61.107852.9955
30.76531.2399-0.86165.6164-3.85547.11670.1415-0.0169-0.3398-0.0177-0.09820.0630.36820.1957-0.04330.32310.1101-0.0916-0.1349-0.144-0.3023-10.1261-75.423330.5522
42.15250.25840.09844.537-0.67431.26440.1514-0.30610.14490.10640.00120.0373-0.2083-0.0082-0.15260.28070.06810.1719-0.1490.0062-0.2359-7.6465-37.76868.3004
54.36140.8770.56241.93510.99382.30840.12950.04460.2484-0.0588-0.0356-0.0055-0.2512-0.08-0.09390.2145-0.00960.0248-0.12540.1879-0.24424.2953-39.4711-14.9801
61.20362.18292.52234.7075-1.90441.21720.0528-0.2236-0.21420.13240.0275-0.0930.01920.2485-0.08030.0334-0.1603-0.1996-0.00290.0602-0.026919.5366-65.72875.6323
73.24111.36970.192.236-0.75246.97720.2961-0.1109-0.1117-0.0498-0.1527-0.0716-0.27720.3104-0.1434-0.0204-0.3392-0.15860.0204-0.0131-0.30433.5292-42.5153-10.6573
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}
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|1476 A|2227 - A|2233 A|9000 }

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