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Basic information

Entry
Database: PDB / ID: 5vie
TitleElectrophilic probes for deciphering substrate recognition by O-GlcNAc transferase
Components
  • CKII
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc Transferase / Electrophilic Probes / complex
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance ...negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / regulation of chromosome separation / positive regulation of aggrephagy / WNT mediated activation of DVL / Condensation of Prometaphase Chromosomes / protein kinase CK2 complex / symbiont-mediated disruption of host cell PML body / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / Receptor Mediated Mitophagy / Formation of WDR5-containing histone-modifying complexes / regulation of synapse assembly / Synthesis of PC / Sin3-type complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / negative regulation of signal transduction by p53 class mediator / Maturation of hRSV A proteins / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / negative regulation of apoptotic signaling pathway / positive regulation of proteolysis / histone acetyltransferase complex / positive regulation of Wnt signaling pathway / negative regulation of double-strand break repair via homologous recombination / positive regulation of lipid biosynthetic process / mitophagy / : / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of TORC1 signaling / response to nutrient / negative regulation of protein ubiquitination / negative regulation of cell migration / positive regulation of translation / Signal transduction by L1 / cell projection / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / Hsp90 protein binding / cellular response to glucose stimulus / response to insulin / protein processing / PML body / chromatin DNA binding / Regulation of necroptotic cell death / mitochondrial membrane / Wnt signaling pathway / Regulation of PTEN stability and activity / positive regulation of protein catabolic process / kinase activity / KEAP1-NFE2L2 pathway / UCH proteinases / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / rhythmic process / double-strand break repair / positive regulation of cold-induced thermogenesis / HATs acetylate histones / chromatin organization / positive regulation of cell growth / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / negative regulation of translation / protein stabilization / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / apoptotic process / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. ...UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Casein Kinase 2, subunit alpha / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-9C1 / Chem-9CD / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Casein kinase II subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJiang, J. / Li, B. / Hu, C.-W. / Worth, M. / Fan, D. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Electrophilic probes for deciphering substrate recognition by O-GlcNAc transferase.
Authors: Hu, C.W. / Worth, M. / Fan, D. / Li, B. / Li, H. / Lu, L. / Zhong, X. / Lin, Z. / Wei, L. / Ge, Y. / Li, L. / Jiang, J.
History
DepositionApr 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_validate_close_contact.auth_atom_id_2 / _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_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jul 21, 2021Group: Author supporting evidence / Derived calculations / Structure summary
Category: chem_comp / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _pdbx_audit_support.funding_organization / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: CKII
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: CKII
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,0838
Polymers164,7464
Non-polymers1,3374
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8970 Å2
ΔGint-55 kcal/mol
Surface area49980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.734, 200.025, 152.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGMETMETAA338 - 102630 - 718
21ARGARGMETMETCC338 - 102630 - 718
12TYRTYRASNASNBB13 - 241 - 12
22TYRTYRASNASNDD13 - 241 - 12

NCS ensembles :
ID
2
1

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGT


Mass: 80974.508 Da / Num. of mol.: 2 / Fragment: UNP residues 323-1041
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli (E. coli) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide CKII


Mass: 1398.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68400*PLUS

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Sugars , 2 types, 2 molecules

#4: Sugar ChemComp-9C1 / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-beta-D-glucose / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-D-glucose / 2-{[(2E)-4-chlorobut-2-enoyl]amino}-2-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 281.690 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16ClNO6
#5: Sugar ChemComp-9CD / 2-{[(2E)-but-2-enoyl]amino}-2-deoxy-beta-D-glucopyranose / 2-{[(2E)-but-2-enoyl]amino}-2-deoxy-beta-D-glucose / 2-{[(2E)-but-2-enoyl]amino}-2-deoxy-D-glucose / 2-{[(2E)-but-2-enoyl]amino}-2-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 247.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO6

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Non-polymers , 2 types, 179 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.08 M Tris (pH 8.5), 0.02 M sodium cacodylate trihydrate (pH 6.5), 1.24 M ammonium sulfate, and 6% w/v polyethylene glycol 8,000.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.6→50.01 Å / Num. obs: 68209 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.053 / Net I/σ(I): 13.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.95 / Num. unique obs: 6807 / CC1/2: 0.878 / Rpim(I) all: 0.321 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE3

3pe3


Resolution: 2.6→50.01 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.87 / SU B: 14.48 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 0.654 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30804 2906 5 %RANDOM
Rwork0.24755 ---
obs0.2506 55742 89.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.891 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.39 Å2
Refinement stepCycle: 1 / Resolution: 2.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10695 0 83 177 10955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01911056
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9751.96315011
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.40751356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86124.513503
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.752151865
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2291556
X-RAY DIFFRACTIONr_chiral_restr0.130.21662
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218374
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2434.0655427
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.176.0856767
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9254.2985629
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined10.53837.9647650
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A17020.13
12C17020.13
21B200.17
22D200.17
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 121 -
Rwork0.337 2443 -
obs--53.53 %

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