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- PDB-5nv4: UDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium ther... -

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Basic information

Entry
Database: PDB / ID: 5nv4
TitleUDP-Glucose Glycoprotein Glucosyltransferase from Chaetomium thermophilum double mutant D611C:G1050C
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
FORMIC ACID / UDP-glucose-glycoprotein glucosyltransferase-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsRoversi, P. / Caputo, A.T. / Hill, J. / Alonzi, D.S. / Zitzmann, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
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
DepositionMay 3, 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 9, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Aug 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 / 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 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)171,1907
Polymers169,6721
Non-polymers1,5176
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint19 kcal/mol
Surface area62340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.226, 142.162, 186.087
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 169672.484 Da / Num. of mol.: 1 / Mutation: D611C G1050C
Source method: isolated from a genetically manipulated source
Details: Double cysteine mutant
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0048990 / Plasmid: pHLsec / Cell line (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.: 1
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: 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.: 4
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-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 3.05 Å3/Da / Density % sol: 59.66 % / Description: A flat prism
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus HT Screen Condition G2 0.1M Carboxylic Acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M ...Details: Morpheus HT Screen Condition G2 0.1M Carboxylic Acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Sodium potassium tartrate tetrahydrate; 0.2M Sodium oxamate) 0.1M Buffer System 1 pH6.5 (Sodium HEPES; MOPS (acid)) 50% v/v Precipitant Mix 2 (40% v/v Ethylene glycol; 20 % w/v PEG 8000)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Apr 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.78→77.85 Å / Num. obs: 53071 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 103.9 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.069 / Net I/σ(I): 7.8
Reflection shellResolution: 2.78→2.93 Å / Redundancy: 5.2 % / Rmerge(I) obs: 3.892 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7648 / CC1/2: 0.412 / Rpim(I) all: 1.826 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSMay 1, 2016data reduction
Aimless0.5.29data scaling
MOLREP11.4.06phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5N2J

5n2j


Resolution: 2.78→77.85 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.921 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.838 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.773 / SU Rfree Blow DPI: 0.309 / SU Rfree Cruickshank DPI: 0.318
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2510 4.83 %RANDOM
Rwork0.239 ---
obs0.239 51917 97.8 %-
Displacement parametersBiso mean: 109.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.0516 Å20 Å20 Å2
2---15.5706 Å20 Å2
3---15.6222 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: 1 / Resolution: 2.78→77.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11066 0 98 34 11198
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00811439HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1815528HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4011SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes290HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1645HARMONIC5
X-RAY DIFFRACTIONt_it11439HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.63
X-RAY DIFFRACTIONt_other_torsion17.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1474SEMIHARMONIC5
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_contact12940SEMIHARMONIC4
LS refinement shellResolution: 2.78→2.85 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 164 5.13 %
Rwork0.299 3033 -
all0.299 3197 -
obs--82.39 %
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)
13.26350.99840.81120.93530.45793.4904-0.1086-0.00810.0175-0.0823-0.1981-0.54420.20830.54420.3068-0.3040.152-0.01740.3040.152-0.138644.2962-1.9336.4977
21.70420.2903-0.80382.18080.22212.99880.1170.09410.12070.14980.0980.1998-0.5442-0.1649-0.215-0.30.1520.0080.3040.0409-0.304-5.008910.226944.9732
32.2034-0.34360.76461.3764-0.28976.3573-0.1072-0.49-0.2468-0.2457-0.0033-0.23820.34110.2950.1106-0.28990.07490.06250.23360.0733-0.175326.359-12.495636.5474
43.2793-0.47091.08991.5864-1.34144.824-0.0214-0.001-0.1238-0.06130.0644-0.02630.4776-0.259-0.043-0.0391-0.14460.04780.1835-0.0605-0.17136.9526-17.6774-1.6392
51.16830.16191.69861.3717-0.6587.4912-0.0280.4471-0.0523-0.2554-0.0674-0.09850.09190.12080.0954-0.24560.02120.05460.304-0.0472-0.126517.007-1.14-19.4495
63.0776-1.70490.86340.7403-0.65283.4515-0.0243-0.1944-0.01010.3616-0.1718-0.0492-0.5183-0.01240.19610.0124-0.0946-0.03670.304-0.0302-0.113118.978616.271112.9562
71.1749-1.3147-0.02581.5523-0.42693.9548-0.04380.2430.0368-0.0557-0.05330.2269-0.5442-0.26550.0971-0.17370.1341-0.10370.2926-0.0004-0.1435.599426.0137-14.4454
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|1474 A|2227 A|2227 }

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