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- PDB-4ay5: Human O-GlcNAc transferase (OGT) in complex with UDP and glycopeptide -

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Basic information

Entry
Database: PDB / ID: 4ay5
TitleHuman O-GlcNAc transferase (OGT) in complex with UDP and glycopeptide
Components
  • GTAB1TIDE
  • UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
KeywordsTRANSFERASE/PEPTIDE / TRANSFERASE-PEPTIDE COMPLEX / TRANSFERASE / GLYCOSYL TRANSFERASE / TRIMERIC PRODUCT COMPLEX / O-GLCNAC
Function / homology
Function and homology information


protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / cardiac septum development / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance ...protein N-acetylglucosaminyltransferase complex / protein O-GlcNAc transferase / regulation of insulin receptor signaling pathway / protein O-acetylglucosaminyltransferase activity / positive regulation of transcription from RNA polymerase II promoter by glucose / cardiac septum development / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / negative regulation of stem cell population maintenance / protein O-linked glycosylation / coronary vasculature development / NSL complex / : / aorta development / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of glycolytic process / RIPK1-mediated regulated necrosis / regulation of synapse assembly / regulation of gluconeogenesis / protein serine/threonine phosphatase activity / mitogen-activated protein kinase p38 binding / positive regulation of stem cell population maintenance / Formation of WDR5-containing histone-modifying complexes / non-canonical NF-kappaB signal transduction / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / mitophagy / hemopoiesis / enzyme activator activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / heart morphogenesis / negative regulation of protein ubiquitination / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / positive regulation of TORC1 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / protein serine/threonine kinase activator activity / response to nutrient / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / positive regulation of translation / TNFR1-induced NF-kappa-B signaling pathway / cell projection / activated TAK1 mediates p38 MAPK activation / cellular response to glucose stimulus / mitochondrial membrane / lung development / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / TAK1-dependent IKK and NF-kappa-B activation / response to insulin / NOD1/2 Signaling Pathway / positive regulation of protein serine/threonine kinase activity / Regulation of necroptotic cell death / chromatin DNA binding / protein processing / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / Interleukin-1 signaling / UCH proteinases / chromatin organization / positive regulation of cold-induced thermogenesis / HATs acetylate histones / in utero embryonic development / positive regulation of MAPK cascade / molecular adaptor activity / endosome membrane / Ub-specific processing proteases / nuclear speck / glutamatergic synapse / apoptotic process / protein-containing complex binding / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Protein phosphatase 2C / TPR repeat / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. ...Signal recognition particle alu RNA binding heterodimer, srp9/1 - #150 / Rossmann fold - #11380 / Signal recognition particle alu RNA binding heterodimer, srp9/1 / O-GlcNAc transferase, C-terminal / Glycosyl transferase family 41 / Protein phosphatase 2C / TPR repeat / Protein phosphatase 2C family / Serine/threonine phosphatases, family 2C, catalytic domain / PPM-type phosphatase domain profile. / PPM-type phosphatase-like domain / PPM-type phosphatase-like domain superfamily / Tetratricopeptide repeat / Tetratricopeptide repeat 1 / 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
URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / TGF-beta-activated kinase 1 and MAP3K7-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3.15 Å
AuthorsSchimpl, M. / Zheng, X. / Blair, D.E. / Schuettelkopf, A.W. / Navratilova, I. / Aristotelous, T. / Ferenbach, A.T. / Macnaughtan, M.A. / Borodkin, V.S. / van Aalten, D.M.F.
CitationJournal: Nat.Chem.Biol. / Year: 2012
Title: O-Glcnac Transferase Invokes Nucleotide Sugar Pyrophosphate Participation in Catalysis
Authors: Schimpl, M. / Zheng, X. / Borodkin, V.S. / Blair, D.E. / Ferenbach, A.T. / Schuettelkopf, A.W. / Navratilova, I. / Aristotelous, T. / Albarbarawi, O. / Robinson, D.A. / Macnaughtan, M.A. / Van Aalten, D.M.F.
History
DepositionJun 18, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
B: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
C: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
D: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
I: GTAB1TIDE
J: GTAB1TIDE
K: GTAB1TIDE
L: GTAB1TIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,88416
Polymers328,3838
Non-polymers2,5018
Water0
1
A: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
I: GTAB1TIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7214
Polymers82,0962
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8.8 kcal/mol
Surface area33680 Å2
MethodPISA
2
B: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
J: GTAB1TIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7214
Polymers82,0962
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-8.4 kcal/mol
Surface area33650 Å2
MethodPISA
3
C: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
K: GTAB1TIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7214
Polymers82,0962
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8.6 kcal/mol
Surface area33770 Å2
MethodPISA
4
D: UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT
L: GTAB1TIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7214
Polymers82,0962
Non-polymers6252
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-8.7 kcal/mol
Surface area33760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)274.170, 274.170, 142.150
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
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A312 - 1028
2111B312 - 1028
3111C312 - 1028
4111D312 - 1028
1211A1201
2211B1201
3211C1201
4211D1201
1311A1202
2311B1202
3311C1202
4311D1202

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.043472, 0.351789, 0.935069), (-0.908013, -0.404275, 0.109881), (0.41668, -0.844278, 0.337004)108.80439, 75.52757, 2.92927
3given(-0.281134, -0.78121, -0.557382), (0.184436, -0.613963, 0.767485), (-0.941778, 0.112965, 0.31669)240.95502, -61.27854, 112.21011
4given(-0.783716, 0.494186, 0.376258), (0.499611, 0.141663, 0.854588), (0.369024, 0.857736, -0.357925)285.784, -131.40971, 9.26081

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Components

#1: Protein
UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N-ACETYLGLUCOSAMINYL TRANSFERASE 110 KDA SUBUNIT / O-GLCNAC TRANSFERASE SUBUNIT P110 / O-LINKED N-ACETYL GLUCOSAMINE TRANSFERASE 110 KDA SUBUNIT / OGT


Mass: 80974.508 Da / Num. of mol.: 4
Fragment: TPR (TRUNCATED) AND CATALYTIC DOMAIN, RESIDUES 313-1031
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ARCTICEXPRESS (RIL) / References: UniProt: O15294, protein O-GlcNAc transferase
#2: Protein/peptide
GTAB1TIDE


Mass: 1121.198 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: UniProt: Q15750*PLUS
#3: Chemical
ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Sequence detailsCHAINS I, J, K, AND L ARE GTAB1TIDE, A SYNTHETIC GLYCOPEPTIDE BASED ON RESIDUES 389-399 OF HUMAN ...CHAINS I, J, K, AND L ARE GTAB1TIDE, A SYNTHETIC GLYCOPEPTIDE BASED ON RESIDUES 389-399 OF HUMAN TAB1 PROTEIN, UNIPROT Q15750, WITH O-LINKED N-ACETYLGLUCOSAMINE LINKED TO SER395.

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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: 4.7 Å3/Da / Density % sol: 73.81 % / Description: NONE
Crystal growpH: 9.3 / Details: 1.45 M K2HPO4, 10 MM EDTA, 1% XYLITOL, pH 9.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. obs: 105108 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.7

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Processing

SoftwareName: REFMAC / Version: 5.6.0117 / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.15→237.44 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.759 / SU ML: 0.223 / Cross valid method: THROUGHOUT / ESU R: 0.673 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 715-718 AND 747-761 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.20391 501 0.5 %RANDOM
Rwork0.17384 ---
obs0.17398 105108 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.844 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å21.11 Å20 Å2
2--2.23 Å20 Å2
3----3.34 Å2
Refinement stepCycle: LAST / Resolution: 3.15→237.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22368 0 156 0 22524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223048
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.97631284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72752780
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.54924.5591044
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.979153904
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.46215120
X-RAY DIFFRACTIONr_chiral_restr0.1160.23468
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02117448
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Ens-ID: 1 / Number: 5631 / Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Dom-IDAuth asym-IDRms dev position (Å)
1A9.87
2B8.56
3C8.08
4D12.23
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 36 -
Rwork0.281 7473 -
obs--99.88 %

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