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- PDB-4xif: Human OGT in complex with UDP-5S-GlcNAc and substrate peptide (ke... -

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Basic information

Entry
Database: PDB / ID: 4xif
TitleHuman OGT in complex with UDP-5S-GlcNAc and substrate peptide (keratin-7)
Components
  • Keratin, type II cytoskeletal 7
  • UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
KeywordsTRANSFERASE / O-GlcNAc transferase Inverting GT-B Substrate complex
Function / homology
Function and homology information


cornification / keratin filament / Keratinization / 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 / acetylglucosaminyltransferase activity / regulation of necroptotic process ...cornification / keratin filament / Keratinization / 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 / acetylglucosaminyltransferase activity / regulation of necroptotic process / regulation of Rac protein signal transduction / Formation of the cornified envelope / negative regulation of stem cell population maintenance / protein O-linked glycosylation / NSL complex / : / intermediate filament / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / regulation of glycolytic process / 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 / keratinization / positive regulation of proteolysis / phosphatidylinositol-3,4,5-trisphosphate binding / mitophagy / hemopoiesis / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / histone acetyltransferase complex / positive regulation of lipid biosynthetic process / negative regulation of protein ubiquitination / positive regulation of TORC1 signaling / viral process / response to nutrient / negative regulation of cell migration / positive regulation of translation / cell projection / 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 / chromatin organization / positive regulation of cold-induced thermogenesis / HATs acetylate histones / glutamatergic synapse / apoptotic process / regulation of transcription by RNA polymerase II / 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 / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Keratin, type II / Keratin type II head / Keratin type II head / : / 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 / Intermediate filament protein, conserved site ...Keratin, type II / Keratin type II head / Keratin type II head / : / 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 / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / TPR repeat / 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
Chem-12V / UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit / Keratin, type II cytoskeletal 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: Keratin, type II cytoskeletal 7
F: Keratin, type II cytoskeletal 7
G: Keratin, type II cytoskeletal 7
H: Keratin, type II cytoskeletal 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)330,97716
Polymers328,0998
Non-polymers2,8788
Water0
1
A: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
E: Keratin, type II cytoskeletal 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7444
Polymers82,0252
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
F: Keratin, type II cytoskeletal 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7444
Polymers82,0252
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
G: Keratin, type II cytoskeletal 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7444
Polymers82,0252
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit
H: Keratin, type II cytoskeletal 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7444
Polymers82,0252
Non-polymers7192
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)275.138, 275.138, 143.136
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
12A
22B
32C
42D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A312 - 1031
2111B312 - 1031
3111C312 - 1031
4111D312 - 1031
1121A2007 - 2017
2121B2007 - 2017
3121C2007 - 2017
4121D2007 - 2017

NCS ensembles :
ID
1
2

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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
Keratin, type II cytoskeletal 7 / / Cytokeratin-7 / CK-7 / Keratin-7 / K7 / Sarcolectin / Type-II keratin Kb7


Mass: 1050.147 Da / Num. of mol.: 4 / Fragment: UNP residues 8-16 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08729
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: 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: 2.95 Å3/Da / Density % sol: 58.34 %
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: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.2→25 Å / Num. obs: 105151 / % possible obs: 99 % / Redundancy: 1.7 % / Net I/σ(I): 1.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
SCALEPACKdata scaling
DENZOdata reduction
REFMACphasing
RefinementResolution: 3.2→25 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.884 / SU B: 17.745 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 1.052 / ESU R Free: 0.365 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23893 1015 1 %RANDOM
Rwork0.2157 ---
obs0.21593 100304 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.604 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20.73 Å2-0 Å2
2--1.46 Å2-0 Å2
3----2.18 Å2
Refinement stepCycle: 1 / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22432 0 176 0 22608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02223124
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3561.96531384
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60852836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6624.4871052
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.733153940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.26915124
X-RAY DIFFRACTIONr_chiral_restr0.0870.23484
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02117484
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_it0.6881.514264
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.413223040
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9138860
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4964.58344
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A5535tight positional0.050.05
11B5535tight positional0.050.05
11C5535tight positional0.040.05
11D5535tight positional0.050.05
22A73tight positional0.040.05
22B73tight positional0.030.05
22C73tight positional0.030.05
22D73tight positional0.030.05
11A5535tight thermal0.080.5
11B5535tight thermal0.080.5
11C5535tight thermal0.10.5
11D5535tight thermal0.080.5
22A73tight thermal0.060.5
22B73tight thermal0.040.5
22C73tight thermal0.050.5
22D73tight thermal0.050.5
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 79 -
Rwork0.331 7227 -
obs--99.16 %

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