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- PDB-4xi9: Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2) -

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Basic information

Entry
Database: PDB / ID: 4xi9
TitleHuman OGT in complex with UDP-5S-GlcNAc and substrate peptide (RBL2)
Components
  • Retinoblastoma-like protein 2
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc transferase inverting GT-B substrate 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-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 non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / 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 / regulation of gluconeogenesis / regulation of glycolytic process / RIPK1-mediated regulated necrosis / Formation of WDR5-containing histone-modifying complexes / regulation of synapse assembly / hemopoiesis / positive regulation of stem cell population maintenance / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / histone acetyltransferase complex / mitophagy / cell projection / response to nutrient / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / 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 / 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 / fusion of virus membrane with host plasma membrane / apoptotic process / viral envelope / regulation of transcription by RNA polymerase II / symbiont entry into host cell / positive regulation of DNA-templated transcription / virion attachment to host cell / host cell plasma membrane / negative regulation of transcription by RNA polymerase II / virion membrane / glutamatergic synapse / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / TLV/ENV coat polyprotein / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat ...F-MuLV receptor-binding / ENV polyprotein (coat polyprotein) / Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110kDa subunit / Rossmann fold - #11380 / TLV/ENV coat polyprotein / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-12V / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å
AuthorsSchimpl, M. / van Aalten, D.M.F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustWT087590MA United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The active site of O-GlcNAc transferase imposes constraints on substrate sequence.
Authors: Pathak, S. / Alonso, J. / Schimpl, M. / Rafie, K. / Blair, D.E. / Borodkin, V.S. / Schuttelkopf, A.W. / Albarbarawi, O. / van Aalten, D.M.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
E: Retinoblastoma-like protein 2
F: Retinoblastoma-like protein 2
G: Retinoblastoma-like protein 2
H: Retinoblastoma-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,37112
Polymers326,8778
Non-polymers2,4944
Water00
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
E: Retinoblastoma-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3433
Polymers81,7192
Non-polymers6231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: Retinoblastoma-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3433
Polymers81,7192
Non-polymers6231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
G: Retinoblastoma-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3433
Polymers81,7192
Non-polymers6231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: Retinoblastoma-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3433
Polymers81,7192
Non-polymers6231
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.910, 273.910, 142.930
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 312 - 1028 / Label seq-ID: 4 - 720

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#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.: 4 / 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
Retinoblastoma-like protein 2 / 130 kDa retinoblastoma-associated protein / p130 / Retinoblastoma-related protein 2 / RBR-2 / pRb2


Mass: 744.833 Da / Num. of mol.: 4 / Fragment: UNP residues 416-422 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q08999
#3: Chemical
ChemComp-12V / (2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate / URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE


Mass: 623.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O16P2S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.74 Å3/Da / Density % sol: 74.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.45 M potassium phosphate, 10 mM EDTA, 1% (w/v) xylitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.922 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.922 Å / Relative weight: 1
ReflectionResolution: 3.1→25 Å / Num. obs: 108153 / % possible obs: 99.7 % / Redundancy: 3.8 % / Net I/σ(I): 9.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
SCALEPACKdata scaling
MOSFLMdata reduction
MOLREPphasing
RefinementResolution: 3.1→25 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.892 / SU B: 14.547 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.697 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22346 2196 2 %RANDOM
Rwork0.20264 ---
obs0.20307 108153 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.873 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20.51 Å2-0 Å2
2--1.02 Å2-0 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22244 0 156 0 22400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02222916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3521.96531112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.64652804
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.16624.5591044
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33153924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.82115120
X-RAY DIFFRACTIONr_chiral_restr0.0880.23468
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02117324
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_it0.7771.514116
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.575222840
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.09638800
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8954.58272
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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

Dom-ID: 1 / Ens-ID: 1 / Number: 5514 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.040.05
Btight positional0.050.05
Ctight positional0.050.05
Dtight positional0.040.05
Atight thermal0.070.5
Btight thermal0.070.5
Ctight thermal0.070.5
Dtight thermal0.080.5
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.415 151 -
Rwork0.313 7789 -
obs--97.88 %

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