[English] 日本語
Yorodumi
- PDB-5l0r: human POGLUT1 in complex with Notch1 EGF12 and UDP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l0r
Titlehuman POGLUT1 in complex with Notch1 EGF12 and UDP
Components
  • Neurogenic locus notch homolog protein 1
  • Protein O-glucosyltransferase 1
KeywordsTRANSFERASE / transferase 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 / coronary vein morphogenesis / negative regulation of collagen biosynthetic process / cardiac vascular smooth muscle cell development / negative regulation of myotube differentiation / somatic stem cell division / left/right axis specification / circulatory system development / negative regulation of cardiac muscle hypertrophy / negative regulation of cell adhesion molecule production / positive regulation of endothelial cell differentiation / interleukin-17-mediated signaling pathway / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / endocardium development / apoptotic process involved in embryonic digit morphogenesis / positive regulation of cardiac epithelial to mesenchymal transition / Pre-NOTCH Processing in Golgi / cardiac epithelial to mesenchymal transition / negative regulation of calcium ion-dependent exocytosis / glucosyltransferase activity / cardiac muscle cell myoblast differentiation / cellular response to follicle-stimulating hormone stimulus / pericardium morphogenesis / cardiac atrium morphogenesis / negative regulation of catalytic activity / neuronal stem cell population maintenance / tissue regeneration / tube formation / paraxial mesoderm development / negative regulation of oligodendrocyte differentiation / regulation of stem cell proliferation / endoderm development / positive regulation of astrocyte differentiation / calcium-ion regulated exocytosis / pulmonary valve morphogenesis / heart trabecula morphogenesis / negative regulation of biomineral tissue development / coronary artery morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / axial mesoderm development / prostate gland epithelium morphogenesis / 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 / SYNCHROTRON / Resolution: 1.5 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
DepositionJul 28, 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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / 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 1.3Mar 24, 2021Group: Source and taxonomy / Structure summary / Category: chem_comp / entity_src_gen
Item: _chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line ..._chem_comp.pdbx_synonyms / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain

-
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)47,6168
Polymers46,6022
Non-polymers1,0146
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-36 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.580, 73.560, 83.280
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, 4 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
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: 4524.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NOTCH1, TAN1 / Plasmid: pMal / Production host: Escherichia coli BL21(DE3) (bacteria) / 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.: 2
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 , 5 types, 355 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG5000 MME, 50 mM MES pH 6.5, 2mM CaCl2, 250mM NaCl, 5% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 68848 / % possible obs: 98 % / Redundancy: 5.7 % / Biso Wilson estimate: 17.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.19
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 1.64 / CC1/2: 0.661 / % possible all: 91

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 1.5→43.448 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.7
RfactorNum. reflection% reflectionSelection details
Rfree0.1707 3442 5 %0
Rwork0.1489 ---
obs0.15 68829 98.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 156.43 Å2 / Biso mean: 32.5202 Å2 / Biso min: 12.15 Å2
Refinement stepCycle: final / Resolution: 1.5→43.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3249 0 89 351 3689
Biso mean--25.35 37.46 -
Num. residues----396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133467
X-RAY DIFFRACTIONf_angle_d1.2994716
X-RAY DIFFRACTIONf_chiral_restr0.072488
X-RAY DIFFRACTIONf_plane_restr0.01601
X-RAY DIFFRACTIONf_dihedral_angle_d14.8932080
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52060.27091180.30452248236686
1.5206-1.54230.28711280.28042416254491
1.5423-1.56530.30381360.25532594273099
1.5653-1.58980.25591370.237325992736100
1.5898-1.61580.24421380.218126232761100
1.6158-1.64370.21931410.206826602801100
1.6437-1.67360.18411370.196826172754100
1.6736-1.70580.19861390.188626412780100
1.7058-1.74060.18541380.172426142752100
1.7406-1.77840.2091380.168426412779100
1.7784-1.81980.17021390.158826442783100
1.8198-1.86530.18361380.151526192757100
1.8653-1.91580.16471400.141426492789100
1.9158-1.97210.18881380.140726282766100
1.9721-2.03580.16251390.137626482787100
2.0358-2.10850.13521380.136626182756100
2.1085-2.1930.15651410.131826792820100
2.193-2.29280.16581370.13172606274399
2.2928-2.41360.1441400.12752658279899
2.4136-2.56480.15161390.13372642278199
2.5648-2.76280.17341400.1392643278399
2.7628-3.04080.18221390.13972652279198
3.0408-3.48070.14131390.13632646278597
3.4807-4.38460.15371400.12372660280097
4.3846-43.46640.17021450.15682742288796
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)
13.6322-0.92270.7210.9968-0.27621.7436-0.1191-0.35540.020.08860.14570.17290.0628-0.6882-0.05020.1923-0.02380.02240.4228-0.00230.15783.585729.799534.6921
22.1412-0.6658-0.35292.9602-0.80194.2746-0.0006-0.2222-0.2451-0.0102-0.0418-0.13520.5580.51480.02060.26010.129-0.05930.3141-0.00890.258732.185412.643231.973
31.7689-0.59710.27721.5173-0.70143.34390.0377-0.1566-0.15110.0740.0978-0.02480.26670.1864-0.08090.15110.0299-0.02260.1351-0.01490.142423.759719.74926.658
43.1272-1.2184-0.24181.05210.71971.3376-0.03250.16020.4674-0.1660.0611-0.1042-0.4290.1191-0.02340.2319-0.03590.01450.10870.01270.212819.81838.810316.0966
53.06030.16940.50272.47461.19572.78660.11030.29150.0245-0.0332-0.13630.1945-0.077-0.30810.00950.12060.0060.00820.1890.01580.10583.318929.73418.8107
64.17981.0965-0.09080.57980.83092.69780.19060.8387-0.4308-0.1122-0.0926-0.01780.1197-0.0999-0.10130.16410.0082-0.0290.2532-0.05720.12958.792622.0782.6479
71.7601-0.0857-0.02890.83810.12172.61740.0390.04080.01960.00120.02280.0291-0.0553-0.1597-0.06580.12170.0038-0.00390.10760.00310.12318.218929.364317.4971
83.7809-1.67260.11857.8451.07694.17180.02780.3092-0.11920.0182-0.06850.41120.0506-0.60120.03220.1267-0.0120.00880.28010.00620.1672-6.472828.25816.8414
95.5025-1.27866.08122.6455-1.20327.0694-0.2318-0.44040.72750.25480.09080.1753-0.4529-0.47570.1960.24020.06230.03520.1735-0.02220.22814.111840.421525.5226
103.4555-1.59420.52072.6553-0.91472.3621-0.1081-0.3908-0.04850.24950.1054-0.26380.07140.44990.04960.19970.0351-0.0480.3209-0.03660.175530.306722.738335.2708
119.27121.2831-1.96875.65022.33566.6112-0.0276-0.013-0.61990.2361-0.05280.08180.72150.16240.14840.23940.0422-0.01560.1722-0.03140.164224.93217.25747.9705
127.67121.70443.61073.68552.35452.4337-0.0491-0.1759-1.59160.65740.0246-0.81921.85160.09210.30180.59350.07780.02170.2497-0.02290.433329.475112.11148.9572
137.0509-1.4967-1.79365.96481.62731.99920.24380.04610.4785-0.26130.4209-0.4611-0.25121.13-0.60590.2352-0.02070.04170.38-0.06930.275636.016224.0255.3921
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 176 )A105 - 176
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 197 )A177 - 197
5X-RAY DIFFRACTION5chain 'A' and (resid 198 through 227 )A198 - 227
6X-RAY DIFFRACTION6chain 'A' and (resid 228 through 248 )A228 - 248
7X-RAY DIFFRACTION7chain 'A' and (resid 249 through 311 )A249 - 311
8X-RAY DIFFRACTION8chain 'A' and (resid 312 through 331 )A312 - 331
9X-RAY DIFFRACTION9chain 'A' and (resid 332 through 349 )A332 - 349
10X-RAY DIFFRACTION10chain 'A' and (resid 350 through 385 )A350 - 385
11X-RAY DIFFRACTION11chain 'B' and (resid 452 through 470 )B452 - 470
12X-RAY DIFFRACTION12chain 'B' and (resid 471 through 477 )B471 - 477
13X-RAY DIFFRACTION13chain '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