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- PDB-8cm9: Structure of human O-GlcNAc transferase in complex with UDP and tP11 -

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Basic information

Entry
Database: PDB / ID: 8cm9
TitleStructure of human O-GlcNAc transferase in complex with UDP and tP11
Components
  • PHE-MET-PRO-LYS-TYR-SER-ILE
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc / OGT / 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 glycolytic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / histone acetyltransferase complex / mitophagy / positive regulation of lipid biosynthetic process / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / response to nutrient / negative regulation of cell migration / cell projection / positive regulation of translation / cellular response to glucose stimulus / mitochondrial membrane / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / response to insulin / Regulation of necroptotic cell death / chromatin DNA binding / protein processing / UCH proteinases / positive regulation of cold-induced thermogenesis / chromatin organization / HATs acetylate histones / glutamatergic synapse / regulation of transcription by RNA polymerase II / apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / TPR repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMeek, R.W. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Royal Society180016 United Kingdom
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Phage display uncovers a sequence motif that drives polypeptide binding to a conserved regulatory exosite of O-GlcNAc transferase.
Authors: Alteen, M.G. / Meek, R.W. / Kolappan, S. / Busmann, J.A. / Cao, J. / O'Gara, Z. / Chou, Y. / Derda, R. / Davies, G.J. / Vocadlo, D.J.
History
DepositionFeb 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: 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.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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: PHE-MET-PRO-LYS-TYR-SER-ILE
F: PHE-MET-PRO-LYS-TYR-SER-ILE
G: PHE-MET-PRO-LYS-TYR-SER-ILE
H: PHE-MET-PRO-LYS-TYR-SER-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)329,29212
Polymers327,6758
Non-polymers1,6174
Water4,252236
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
E: PHE-MET-PRO-LYS-TYR-SER-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3233
Polymers81,9192
Non-polymers4041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-18 kcal/mol
Surface area27630 Å2
MethodPISA
2
B: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: PHE-MET-PRO-LYS-TYR-SER-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3233
Polymers81,9192
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-17 kcal/mol
Surface area27410 Å2
MethodPISA
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: PHE-MET-PRO-LYS-TYR-SER-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3233
Polymers81,9192
Non-polymers4041
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-19 kcal/mol
Surface area27630 Å2
MethodPISA
4
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
G: PHE-MET-PRO-LYS-TYR-SER-ILE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3233
Polymers81,9192
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-18 kcal/mol
Surface area27270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)272.970, 272.970, 142.593
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:

Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 322 - 1038 / Label seq-ID: 4 - 720

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111AA
211BB
322AA
422CC
533AA
633DD
744BB
844CC
955BB
1055DD
1166CC
1266DD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

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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: 81032.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OGT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide
PHE-MET-PRO-LYS-TYR-SER-ILE


Mass: 886.089 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.68 Å3/Da / Density % sol: 73.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 M potassium phosphate dibasic, 5 % xylitol and 10 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→122.1 Å / Num. obs: 149701 / % possible obs: 100 % / Redundancy: 21.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.286 / Rpim(I) all: 0.062 / Net I/σ(I): 9.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 22 % / Rmerge(I) obs: 2.647 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 7348 / CC1/2: 0.619 / Rpim(I) all: 0.563

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→122.1 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.931 / SU B: 11.132 / SU ML: 0.201 / Cross valid method: FREE R-VALUE / ESU R: 0.367 / ESU R Free: 0.254
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.224 7627 5.096 %
Rwork0.1964 142053 -
all0.198 --
obs-142053 99.984 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 58.798 Å2
Baniso -1Baniso -2Baniso -3
1-1.269 Å20.635 Å20 Å2
2--1.269 Å2-0 Å2
3----4.118 Å2
Refinement stepCycle: LAST / Resolution: 2.8→122.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22072 0 100 236 22408
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01322733
X-RAY DIFFRACTIONr_bond_other_d0.0010.01521160
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.64630935
X-RAY DIFFRACTIONr_angle_other_deg1.4221.57648691
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.62452836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.48823.2891125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24153700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.42115104
X-RAY DIFFRACTIONr_chiral_restr0.0680.23034
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0225964
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025092
X-RAY DIFFRACTIONr_nbd_refined0.2190.24970
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.220273
X-RAY DIFFRACTIONr_nbtor_refined0.1720.211280
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.210922
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2440
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0450.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.211
X-RAY DIFFRACTIONr_nbd_other0.1760.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1420.25
X-RAY DIFFRACTIONr_mcbond_it5.1876.16211362
X-RAY DIFFRACTIONr_mcbond_other5.1866.16211361
X-RAY DIFFRACTIONr_mcangle_it7.4219.23814186
X-RAY DIFFRACTIONr_mcangle_other7.4219.23914187
X-RAY DIFFRACTIONr_scbond_it5.8596.50311370
X-RAY DIFFRACTIONr_scbond_other5.8526.50311370
X-RAY DIFFRACTIONr_scangle_it8.5049.5916746
X-RAY DIFFRACTIONr_scangle_other8.5019.5916746
X-RAY DIFFRACTIONr_lrange_it11.162117.59698106
X-RAY DIFFRACTIONr_lrange_other11.163117.62298045
X-RAY DIFFRACTIONr_ncsr_local_group_10.0570.0523493
X-RAY DIFFRACTIONr_ncsr_local_group_20.0560.0523588
X-RAY DIFFRACTIONr_ncsr_local_group_30.0560.0523591
X-RAY DIFFRACTIONr_ncsr_local_group_40.0570.0523648
X-RAY DIFFRACTIONr_ncsr_local_group_50.0590.0523546
X-RAY DIFFRACTIONr_ncsr_local_group_60.0550.0523687
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.056980.0501
12BX-RAY DIFFRACTIONLocal ncs0.056980.0501
23AX-RAY DIFFRACTIONLocal ncs0.055750.0501
24CX-RAY DIFFRACTIONLocal ncs0.055750.0501
35AX-RAY DIFFRACTIONLocal ncs0.055740.0501
36DX-RAY DIFFRACTIONLocal ncs0.055740.0501
47BX-RAY DIFFRACTIONLocal ncs0.056510.0501
48CX-RAY DIFFRACTIONLocal ncs0.056510.0501
59BX-RAY DIFFRACTIONLocal ncs0.059320.0501
510DX-RAY DIFFRACTIONLocal ncs0.059320.0501
611CX-RAY DIFFRACTIONLocal ncs0.055260.0501
612DX-RAY DIFFRACTIONLocal ncs0.055260.0501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.8730.3395710.33710387X-RAY DIFFRACTION99.9635
2.873-2.9510.3435510.31110184X-RAY DIFFRACTION99.9814
2.951-3.0370.3085030.2969938X-RAY DIFFRACTION99.9809
3.037-3.130.285030.269607X-RAY DIFFRACTION100
3.13-3.2330.2855170.2429319X-RAY DIFFRACTION99.9898
3.233-3.3470.2635430.2348992X-RAY DIFFRACTION100
3.347-3.4730.2425050.2218679X-RAY DIFFRACTION99.9782
3.473-3.6150.2494440.2198354X-RAY DIFFRACTION99.9773
3.615-3.7750.2324480.2028044X-RAY DIFFRACTION99.9882
3.775-3.960.2313740.1867798X-RAY DIFFRACTION100
3.96-4.1740.1874010.1647282X-RAY DIFFRACTION100
4.174-4.4270.1773330.1496996X-RAY DIFFRACTION100
4.427-4.7320.1673470.1386533X-RAY DIFFRACTION99.9709
4.732-5.1110.1743010.1356148X-RAY DIFFRACTION100
5.111-5.5990.1933230.1545594X-RAY DIFFRACTION99.9831
5.599-6.2590.2062380.1695146X-RAY DIFFRACTION100
6.259-7.2270.2132660.1824484X-RAY DIFFRACTION100
7.227-8.8490.1632040.1463838X-RAY DIFFRACTION100
8.849-12.5050.1461670.1543005X-RAY DIFFRACTION100
12.505-122.10.368880.3491725X-RAY DIFFRACTION99.6154

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