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- PDB-5c1d: Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L) -

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Basic information

Entry
Database: PDB / ID: 5c1d
TitleHuman OGT in complex with UDP-5S-GlcNAc and substrate peptide (RB2L)
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


regulation of lipid kinase activity / negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / FOXO-mediated transcription of cell cycle genes ...regulation of lipid kinase activity / negative regulation of non-canonical inflammasome complex assembly / protein N-acetylglucosaminyltransferase complex / protein O-acetylglucosaminyltransferase activity / RNA polymerase II C-terminal domain S5 O-GlcNAc transferase activity / RNA polymerase II C-terminal domain S7 O-GlcNAc transferase activity / regulation of insulin receptor signaling pathway / protein O-GlcNAc transferase / positive regulation of transcription from RNA polymerase II promoter by glucose / FOXO-mediated transcription of cell cycle genes / acetylglucosaminyltransferase activity / regulation of Rac protein signal transduction / regulation of necroptotic process / negative regulation of stem cell population maintenance / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / protein O-linked glycosylation / NSL complex / Transcription of E2F targets under negative control by DREAM complex / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of synapse assembly / negative regulation of G1/S transition of mitotic cell cycle / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / G1/S-Specific Transcription / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / G0 and Early G1 / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / mitophagy / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of cell migration / positive regulation of translation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cell projection / response to insulin / promoter-specific chromatin binding / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / mitochondrial membrane / cellular response to glucose stimulus / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / Cyclin D associated events in G1 / UCH proteinases / chromatin organization / HATs acetylate histones / positive regulation of cold-induced thermogenesis / chromosome / transcription regulator complex / cell differentiation / negative regulation of gene expression / apoptotic process / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / glutamatergic synapse / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain ...Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal 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 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / Glycogen Phosphorylase B; / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 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 / PHOSPHATE ION / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Retinoblastoma-like protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchimpl, M. / Rafie, K. / van Aalten, D.M.F.
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
DepositionJun 13, 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 1.3Jan 10, 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
Item: _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-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
C: Retinoblastoma-like protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,5335
Polymers81,7192
Non-polymers8133
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-15 kcal/mol
Surface area27830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.527, 151.611, 200.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1240-

HOH

21A-1296-

HOH

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Components

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


Mass: 80974.508 Da / Num. of mol.: 1 / Fragment: UNP residues 313-1031
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli BL21 (bacteria) / 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.: 1 / Fragment: UNP residues 416-423 / Source method: obtained synthetically
Details: Nitrogen from residue 8 results from an acetylation during chemical synthesis of the compound and is part of residue 7 but needed a different residue number in the PDB
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.: 1 / Source method: obtained synthetically / Formula: C17H27N3O16P2S
#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.: 254 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.84 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.45 M Potassium diohydrogen phosphate, 8 mM EDTA, 1% xylitol (reservoir). 1.45 M Potassium diohydrogen phosphate, 8 mM EDTA, 1% xylitol, 0.5 M Ammonium sulfate (drop)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.05→46.2 Å / Num. all: 443970 / Num. obs: 65809 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.826 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Coot0.7.1model building
SCALA3.3.21data scaling
XDS0.5data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PE4

3pe4


Resolution: 2.05→46.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.245 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22864 3160 4.8 %RANDOM
Rwork0.19461 ---
obs0.19625 62649 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å20 Å2
2--4.15 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.05→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5539 0 49 254 5842
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195740
X-RAY DIFFRACTIONr_bond_other_d0.0010.025480
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9657797
X-RAY DIFFRACTIONr_angle_other_deg0.7983.00212617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6575704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.05724.504262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24515981
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8091531
X-RAY DIFFRACTIONr_chiral_restr0.0750.2867
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021308
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_it2.3954.3352820
X-RAY DIFFRACTIONr_mcbond_other2.3954.3352821
X-RAY DIFFRACTIONr_mcangle_it3.5946.4883524
X-RAY DIFFRACTIONr_mcangle_other3.5946.4883524
X-RAY DIFFRACTIONr_scbond_it2.9934.6822915
X-RAY DIFFRACTIONr_scbond_other2.964.672910
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7636.8714262
X-RAY DIFFRACTIONr_long_range_B_refined7.09134.8566763
X-RAY DIFFRACTIONr_long_range_B_other7.07434.7886669
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 221 -
Rwork0.327 4602 -
obs--100 %

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