[English] 日本語
Yorodumi
- PDB-8fe7: Crystal structure of human O-GlcNAc transferase (OGT) in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8fe7
TitleCrystal structure of human O-GlcNAc transferase (OGT) in complex with an exosite-binding peptide (SMG9) and UDP-GlcNAc
Components
  • Nonsense-mediated mRNA decay factor SMG9
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc transferase / exosite / protein-protein interaction / 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 / eye development ...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 / eye development / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of gluconeogenesis / regulation of synapse assembly / Formation of WDR5-containing histone-modifying complexes / Sin3-type complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of stem cell population maintenance / phosphatidylinositol-3,4,5-trisphosphate binding / hemopoiesis / positive regulation of proteolysis / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / mitophagy / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of protein ubiquitination / response to nutrient / positive regulation of TORC1 signaling / negative regulation of cell migration / positive regulation of translation / cell projection / cellular response to glucose stimulus / circadian regulation of gene expression / negative regulation of transforming growth factor beta receptor signaling pathway / response to insulin / brain development / mitochondrial membrane / protein processing / chromatin DNA binding / Regulation of necroptotic cell death / UCH proteinases / positive regulation of cold-induced thermogenesis / HATs acetylate histones / heart development / chromatin organization / in utero embryonic development / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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 / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Nonsense-mediated mRNA decay factor SMG9 / 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 ...Nonsense-mediated mRNA decay factor SMG9 / 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 / Glycogen Phosphorylase B; / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Nonsense-mediated mRNA decay factor SMG9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsXie, J. / Jiang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM121718 United States
CitationJournal: Nat.Chem.Biol. / Year: 2023
Title: Motif-dependent binding on the intervening domain regulates O-GlcNAc transferase.
Authors: Blankenship, C.M. / Xie, J. / Benz, C. / Wang, A. / Ivarsson, Y. / Jiang, J.
History
DepositionDec 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Nonsense-mediated mRNA decay factor SMG9
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Nonsense-mediated mRNA decay factor SMG9
E: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: Nonsense-mediated mRNA decay factor SMG9
G: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: Nonsense-mediated mRNA decay factor SMG9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,21812
Polymers329,7898
Non-polymers2,4294
Water00
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
B: Nonsense-mediated mRNA decay factor SMG9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0543
Polymers82,4472
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-12 kcal/mol
Surface area29040 Å2
MethodPISA
2
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
D: Nonsense-mediated mRNA decay factor SMG9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0543
Polymers82,4472
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-14 kcal/mol
Surface area29540 Å2
MethodPISA
3
E: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: Nonsense-mediated mRNA decay factor SMG9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0543
Polymers82,4472
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-12 kcal/mol
Surface area29200 Å2
MethodPISA
4
G: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: Nonsense-mediated mRNA decay factor SMG9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,0543
Polymers82,4472
Non-polymers6071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-13 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)273.669, 273.669, 143.144
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Space group name HallP32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z

-
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
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
Nonsense-mediated mRNA decay factor SMG9


Mass: 1472.623 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H0W8
#3: Chemical
ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H27N3O17P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.69 Å3/Da / Density % sol: 73.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.9M Ammonium Sulfate, 0.1M Tris pH 8.5, 1% Xylitol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.98→237 Å / Num. obs: 125036 / % possible obs: 99.5 % / Redundancy: 7.7 % / Biso Wilson estimate: 71.89 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.7
Reflection shellResolution: 2.98→3.03 Å / Num. unique obs: 6187 / CC1/2: 0.784

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata processing
Cootmodel building
PHASERphasing
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.98→118.5 Å / SU ML: 0.3779 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.9314
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2174 1987 1.59 %
Rwork0.1862 122984 -
obs0.1867 124971 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.39 Å2
Refinement stepCycle: LAST / Resolution: 2.98→118.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22632 0 156 0 22788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002923324
X-RAY DIFFRACTIONf_angle_d0.600131664
X-RAY DIFFRACTIONf_chiral_restr0.04253496
X-RAY DIFFRACTIONf_plane_restr0.00554112
X-RAY DIFFRACTIONf_dihedral_angle_d4.66773092
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.050.37231420.31958663X-RAY DIFFRACTION99.06
3.05-3.140.33991380.29588681X-RAY DIFFRACTION99.28
3.14-3.230.30791380.28318709X-RAY DIFFRACTION99.33
3.23-3.330.30491370.26478728X-RAY DIFFRACTION98.93
3.33-3.450.25511410.24388714X-RAY DIFFRACTION99.48
3.45-3.590.23611420.21628751X-RAY DIFFRACTION99.21
3.59-3.750.23541400.19848756X-RAY DIFFRACTION99.63
3.75-3.950.22331380.17818772X-RAY DIFFRACTION99.46
3.95-4.20.20791420.17538754X-RAY DIFFRACTION99.53
4.2-4.520.19351440.15168776X-RAY DIFFRACTION99.53
4.52-4.980.16861410.15068831X-RAY DIFFRACTION99.69
4.98-5.70.18281440.17048868X-RAY DIFFRACTION99.78
5.7-7.180.19921460.17658922X-RAY DIFFRACTION99.76
7.18-118.50.18261540.14379059X-RAY DIFFRACTION99.31
Refinement TLS params.Method: refined / Origin x: 106.269849815 Å / Origin y: 27.877457322 Å / Origin z: 25.2237147263 Å
111213212223313233
T0.610289820389 Å20.0126918718204 Å2-0.0153498394264 Å2-0.443467523434 Å2-0.0196675300873 Å2--0.444153916189 Å2
L0.0777662846723 °2-0.0340741985084 °20.00119077839645 °2-0.1748858292 °2-0.092093137904 °2--0.0839634990878 °2
S0.00636507576214 Å °-0.0104254659864 Å °-0.0108475262584 Å °-0.0159911148669 Å °0.0120721269589 Å °0.0112513574715 Å °0.0939864919284 Å °-0.0637377182319 Å °-0.020947359513 Å °
Refinement TLS groupSelection details: all

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more