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- PDB-5lwv: Human OGT in complex with UDP and fused substrate peptide (HCF1) -

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Basic information

Entry
Database: PDB / ID: 5lwv
TitleHuman OGT in complex with UDP and fused substrate peptide (HCF1)
ComponentsHost cell factor 1,UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / glycosylation / signalling / O-GlcNAc / O-GlcNAc transferase / substrate recognition
Function / homology
Function and homology information


negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / release from viral latency / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / 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 non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / release from viral latency / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / protein O-linked glycosylation / negative regulation of stem cell population maintenance / Set1C/COMPASS complex / regulation of gluconeogenesis / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / hemopoiesis / positive regulation of stem cell population maintenance / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / histone methyltransferase complex / positive regulation of proteolysis / MLL1 complex / phosphatidylinositol-3,4,5-trisphosphate binding / histone acetyltransferase complex / regulation of protein-containing complex assembly / mitophagy / cell projection / response to nutrient / positive regulation of TORC1 signaling / negative regulation of protein ubiquitination / positive regulation of cell cycle / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cell migration / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of translation / protein processing / cellular response to glucose stimulus / circadian regulation of gene expression / Transcriptional activation of mitochondrial biogenesis / response to insulin / chromatin DNA binding / Regulation of necroptotic cell death / mitochondrial membrane / UCH proteinases / positive regulation of cold-induced thermogenesis / HATs acetylate histones / chromatin organization / DNA-binding transcription factor binding / protein-macromolecule adaptor activity / transcription coactivator activity / protein stabilization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / cadherin binding / chromatin remodeling / apoptotic process / neuronal cell body / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Host cell factor / : / Host cell factor, Kelch-repeats domain / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat ...Host cell factor / : / Host cell factor, Kelch-repeats domain / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Kelch-type beta propeller / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tetratricopeptide-like helical domain superfamily / Immunoglobulin-like fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Host cell factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRaimi, O. / Rafie, K. / Kapuria, V. / Herr, W. / van Aalten, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110061 United Kingdom
CitationJournal: Open Biol / Year: 2017
Title: Recognition of a glycosylation substrate by the O-GlcNAc transferase TPR repeats.
Authors: Rafie, K. / Raimi, O. / Ferenbach, A.T. / Borodkin, V.S. / Kapuria, V. / van Aalten, D.M.F.
History
DepositionSep 19, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Host cell factor 1,UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4665
Polymers83,7791
Non-polymers6864
Water11,980665
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-19 kcal/mol
Surface area28030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.024, 168.024, 162.265
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1604-

HOH

21A-1814-

HOH

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Components

#1: Protein Host cell factor 1,UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / HCF-1 / C1 factor / CFF / VCAF / VP16 accessory protein / O-GlcNAc transferase subunit p110 / O- ...HCF-1 / C1 factor / CFF / VCAF / VP16 accessory protein / O-GlcNAc transferase subunit p110 / O-linked N-acetylglucosamine transferase 110 kDa subunit / OGT


Mass: 83779.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HCFC1, HCF1, HFC1, OGT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P51610, UniProt: O15294, protein O-GlcNAc transferase
#2: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / 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: 3.98 Å3/Da / Density % sol: 69.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 1.3M Ammonium tartrate diabasic; 0.1M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 13, 2015 / Details: Toroidal mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.9→48.53 Å / Num. obs: 106157 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rsym value: 0.12 / Net I/σ(I): 14.4
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.95 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.684 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 1.9→48.5 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.731 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19933 5042 5 %RANDOM
Rwork0.16943 ---
obs0.17094 95998 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.491 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å2-0.17 Å20 Å2
2---0.35 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5593 0 41 665 6299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0195764
X-RAY DIFFRACTIONr_bond_other_d0.0020.025484
X-RAY DIFFRACTIONr_angle_refined_deg1.9991.9617826
X-RAY DIFFRACTIONr_angle_other_deg1.069312628
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175710
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.84324.583264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6815979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3711530
X-RAY DIFFRACTIONr_chiral_restr0.1270.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216518
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021314
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_it2.8032.7252843
X-RAY DIFFRACTIONr_mcbond_other2.82.7242842
X-RAY DIFFRACTIONr_mcangle_it3.8024.0583549
X-RAY DIFFRACTIONr_mcangle_other3.8024.0593550
X-RAY DIFFRACTIONr_scbond_it4.2943.1492921
X-RAY DIFFRACTIONr_scbond_other4.2753.1442913
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2184.5364265
X-RAY DIFFRACTIONr_long_range_B_refined7.89423.1837196
X-RAY DIFFRACTIONr_long_range_B_other7.89423.1857197
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 391 -
Rwork0.297 6962 -
obs--99.7 %

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