[English] 日本語
Yorodumi
- PDB-5ub5: human POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ub5
Titlehuman POGLUT1 in complex with human Notch1 EGF12 S458T mutant and UDP
Components
  • Neurogenic locus notch homolog protein 1
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / glycosyltransferase / GT-B glucosyltransferase
Function / homology
Function and homology information


EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis ...EGF-domain serine glucosyltransferase / EGF-domain serine xylosyltransferase / EGF-domain serine glucosyltransferase activity / EGF-domain serine xylosyltransferase activity / muscle tissue development / regulation of gastrulation / protein O-linked glycosylation via serine / UDP-xylosyltransferase activity / Defective LFNG causes SCDO3 / coronary sinus valve morphogenesis / cardiac right atrium morphogenesis / cardiac right ventricle formation / growth involved in heart morphogenesis / Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation / cell differentiation in spinal cord / retinal cone cell differentiation / venous endothelial cell differentiation / arterial endothelial cell differentiation / cardiac chamber formation / epithelial cell fate commitment / negative regulation of pro-B cell differentiation / Pre-NOTCH Processing in the Endoplasmic Reticulum / negative regulation of inner ear auditory receptor cell differentiation / mitral valve formation / cell migration involved in endocardial cushion formation / glomerular mesangial cell development / negative regulation of photoreceptor cell differentiation / negative regulation of cell proliferation involved in heart valve morphogenesis / regulation of somitogenesis / inhibition of neuroepithelial cell differentiation / endocardium morphogenesis / atrioventricular node development / foregut morphogenesis / regulation of cell adhesion involved in heart morphogenesis / distal tubule development / MAML1-RBP-Jkappa- ICN1 complex / regulation of epithelial cell proliferation involved in prostate gland development / auditory receptor cell fate commitment / positive regulation of aorta morphogenesis / negative regulation of endothelial cell chemotaxis / neuroendocrine cell differentiation / collecting duct development / negative regulation of extracellular matrix constituent secretion / positive regulation of transcription of Notch receptor target / UDP-glucosyltransferase activity / positive regulation of smooth muscle cell differentiation / cellular response to tumor cell / positive regulation of apoptotic process involved in morphogenesis / compartment pattern specification / vasculogenesis involved in coronary vascular morphogenesis / T-helper 17 type immune response / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / epithelial to mesenchymal transition involved in endocardial cushion formation / regulation of extracellular matrix assembly / endocardial cell differentiation / cardiac ventricle morphogenesis / cardiac left ventricle morphogenesis / mesenchymal cell development / epidermal cell fate specification / negative regulation of collagen biosynthetic process / circulatory system development / coronary vein morphogenesis / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / negative regulation of cell adhesion molecule production / negative regulation of cardiac muscle hypertrophy / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / positive regulation of endothelial cell differentiation / interleukin-17-mediated signaling pathway / apoptotic process involved in embryonic digit morphogenesis / endocardium development / positive regulation of cardiac epithelial to mesenchymal transition / cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / glucosyltransferase activity / negative regulation of calcium ion-dependent exocytosis / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / tissue regeneration / neuronal stem cell population maintenance / tube formation / paraxial mesoderm development / positive regulation of astrocyte differentiation / negative regulation of oligodendrocyte differentiation / endoderm development / regulation of stem cell proliferation / pulmonary valve morphogenesis / calcium-ion regulated exocytosis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / negative regulation of cell-cell adhesion mediated by cadherin / coronary artery morphogenesis / prostate gland epithelium morphogenesis / axial mesoderm development / luteolysis
Similarity search - Function
Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein ...Glycosyl transferase CAP10 domain / Glycosyl transferase family 90 / Putative lipopolysaccharide-modifying enzyme. / Neurogenic locus notch homolog protein 1 / Notch, C-terminal / Domain of unknown function / Notch / Notch, NOD domain / Notch, NODP domain / NOTCH protein / NOTCH protein / NOD / NODP / Notch-like domain superfamily / LNR (Lin-12/Notch) repeat profile. / LNR domain / Notch domain / Domain found in Notch and Lin-12 / EGF-like, conserved site / Human growth factor-like EGF / Calcium-binding EGF domain / Ankyrin repeats (many copies) / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / Ankyrin repeat / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
URIDINE-5'-DIPHOSPHATE / Neurogenic locus notch homolog protein 1 / Protein O-glucosyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.089 Å
AuthorsLi, Z. / Rini, J.M.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis of Notch O-glucosylation and O-xylosylation by mammalian protein-O-glucosyltransferase 1 (POGLUT1).
Authors: Li, Z. / Fischer, M. / Satkunarajah, M. / Zhou, D. / Withers, S.G. / Rini, J.M.
History
DepositionDec 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Apr 4, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.type / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein O-glucosyltransferase 1
B: Neurogenic locus notch homolog protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7247
Polymers46,6162
Non-polymers1,1085
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-9 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.951, 74.072, 83.583
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Protein/peptide / Sugars , 3 types, 5 molecules AB

#1: Protein Protein O-glucosyltransferase 1 / CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes ...CAP10-like 46 kDa protein / hCLP46 / KTEL motif-containing protein 1 / Myelodysplastic syndromes relative protein / O-glucosyltransferase Rumi homolog / hRumi / Protein O-xylosyltransferase


Mass: 42077.117 Da / Num. of mol.: 1 / Fragment: UNP residues 29-385
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: POGLUT1, C3orf9, CLP46, KTELC1, MDSRP, MDS010, UNQ490/PRO1006
Plasmid: PB-T-PAF / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human)
References: UniProt: Q8NBL1, Transferases; Glycosyltransferases; Hexosyltransferases, protein xylosyltransferase
#2: Protein/peptide Neurogenic locus notch homolog protein 1 / hN1 / Translocation-associated notch protein TAN-1


Mass: 4538.979 Da / Num. of mol.: 1 / Fragment: UNP residues 452-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P46531
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

-
Non-polymers , 3 types, 339 molecules

#4: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% (v/v) PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% (v/v) 2-methyl-2,4-pentanediol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER TURBO X-RAY SOURCE / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: PIXEL / Date: Nov 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.089→20.9 Å / Num. obs: 26486 / % possible obs: 98.96 % / Redundancy: 11 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09068 / Net I/σ(I): 18.74
Reflection shellResolution: 2.089→2.164 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.5486 / Mean I/σ(I) obs: 3.16 / Num. unique obs: 2401 / CC1/2: 0.826 / % possible all: 91.49

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
SAINTdata scaling
PDB_EXTRACT3.22data extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L0R

5l0r


Resolution: 2.089→20.896 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 1365 5.16 %0
Rwork0.1526 25114 --
obs0.1547 26479 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.98 Å2 / Biso mean: 32.9548 Å2 / Biso min: 6.44 Å2
Refinement stepCycle: final / Resolution: 2.089→20.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 121 337 3704
Biso mean--39.69 35 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123483
X-RAY DIFFRACTIONf_angle_d1.2354752
X-RAY DIFFRACTIONf_chiral_restr0.071496
X-RAY DIFFRACTIONf_plane_restr0.01609
X-RAY DIFFRACTIONf_dihedral_angle_d12.2872072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0887-2.16330.27871160.23692258237490
2.1633-2.24980.24841330.193425042637100
2.2498-2.35210.21291390.164124822621100
2.3521-2.47590.19531360.154425142650100
2.4759-2.63070.22291520.155325102662100
2.6307-2.83340.21430.150425082651100
2.8334-3.11770.19011320.158725382670100
3.1177-3.56690.18771390.141325482687100
3.5669-4.48660.16441450.126925652710100
4.4866-20.89680.16721300.14612687281799
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9881-0.49570.03790.77560.04940.0547-0.1598-0.18570.04350.25140.06590.0150.2015-0.5032-0.21840.191-0.02530.06030.4234-0.01090.12094.096130.397734.9009
20.188-0.0092-0.20680.0197-0.010.2499-0.0749-0.333-0.2480.09120.0338-0.14720.32840.36950.00280.33530.208-0.01590.39330.06380.283232.241112.924531.9428
30.1284-0.024-0.00930.74540.29750.5596-0.0572-0.1373-0.1560.12240.1213-0.1970.31980.38520.03850.23530.0637-0.02090.21710.00050.186727.854120.812328.9275
40.6668-0.35360.08310.40380.30750.52220.0207-0.0441-0.00590.04260.0334-0.02140.07790.10760.19060.14690.01980.01050.07610.00230.148719.83426.107821.8291
50.71060.0271-0.15840.11030.07560.8080.0550.3539-0.0685-0.0284-0.03380.04160.0996-0.34620.08170.1207-0.0063-0.00930.1948-0.04560.13055.547727.11146.2448
60.7324-0.149-0.1960.3367-0.06910.8549-0.01510.00870.07130.01280.00070.06730.0168-0.31230.00630.0922-0.01050.00380.1281-0.00680.10694.878131.532318.8246
70.5383-0.35370.27330.3539-0.34740.8362-0.157-0.44430.07810.14910.178-0.32030.11530.48940.1390.21950.1379-0.01440.33790.01590.176730.084922.903135.4433
80.2486-0.14410.20730.0822-0.11570.1809-0.00980.1402-0.2956-0.0033-0.08060.04340.43420.1862-0.0860.34710.08320.04570.1542-0.08780.268826.221815.55078.1296
90.1014-0.07370.12890.0559-0.09560.16840.17190.15140.0471-0.14540.3893-0.28280.04960.10430.03280.311-0.04860.09050.355-0.08210.30336.266524.49295.5307
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 68 )A30 - 68
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 104 )A69 - 104
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 139 )A105 - 139
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 197 )A140 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 248 )A198 - 248
6X-RAY DIFFRACTION6chain 'A' and (resid 249 through 349 )A249 - 349
7X-RAY DIFFRACTION7chain 'A' and (resid 350 through 385 )A350 - 385
8X-RAY DIFFRACTION8chain 'B' and (resid 452 through 477 )B452 - 477
9X-RAY DIFFRACTION9chain 'B' and (resid 478 through 491 )B478 - 491

+
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