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- PDB-8og4: Exostosin-like 3 UDP complex -

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Basic information

Entry
Database: PDB / ID: 8og4
TitleExostosin-like 3 UDP complex
ComponentsExostosin-like 3
KeywordsTRANSFERASE / Glycosyltransferase / heparan sulfate
Function / homology
Function and homology information


glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / positive regulation of detection of glucose / protein-hormone receptor activity / heparan sulfate proteoglycan biosynthetic process / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / XBP1(S) activates chaperone genes / glycosyltransferase activity / protein glycosylation ...glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / positive regulation of detection of glucose / protein-hormone receptor activity / heparan sulfate proteoglycan biosynthetic process / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / XBP1(S) activates chaperone genes / glycosyltransferase activity / protein glycosylation / negative regulation of cytokine production involved in inflammatory response / negative regulation of inflammatory response / positive regulation of cell growth / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum membrane / Golgi apparatus / magnesium ion binding / endoplasmic reticulum / nucleus / plasma membrane
Similarity search - Function
Exostosin-like / Exostosin, GT47 domain / Exostosin family / Glycosyl transferase 64 domain / Glycosyl transferase family 64 domain / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE / Exostosin-like 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSammon, D. / Hohenester, E.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust101748/Z/13/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T01279X/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Molecular mechanism of decision-making in glycosaminoglycan biosynthesis.
Authors: Sammon, D. / Krueger, A. / Busse-Wicher, M. / Morgan, R.M. / Haslam, S.M. / Schumann, B. / Briggs, D.C. / Hohenester, E.
History
DepositionMar 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Exostosin-like 3
B: Exostosin-like 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,81510
Polymers203,2262
Non-polymers3,5898
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Dimer seen in cryoEM structure (PDB 7au2)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15960 Å2
ΔGint-39 kcal/mol
Surface area53010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.617, 121.617, 259.537
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Exostosin-like 3 / EXT-related protein 1 / Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase ...EXT-related protein 1 / Glucuronyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / Hereditary multiple exostoses gene isolog / Multiple exostosis-like protein 3 / Putative tumor suppressor protein EXTL3


Mass: 101613.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXTL3, EXTL1L, EXTR1, KIAA0519 / Production host: Homo sapiens (human)
References: UniProt: O43909, glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase

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Sugars , 2 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 78 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 12.5% (w/v) PEG3350, 0.1 M malic acid, pH 7.0. Soaked overnight in 15% PEG 3350, 0.1 M malic acid, pH 7.0, 5 mM UDP and 5 mM MnCl2.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9212 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9212 Å / Relative weight: 1
ReflectionResolution: 2.1→55.16 Å / Num. obs: 129790 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 54.46 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.048 / Net I/σ(I): 7.4
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 6395 / CC1/2: 0.255 / Rpim(I) all: 0.986

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Processing

Software
NameVersionClassification
PHENIX1.18rc1_3769refinement
PHENIX1.18rc1_3769refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20.52 Å / SU ML: 0.3258 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.7477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 6094 5.04 %
Rwork0.1921 114827 -
obs0.1941 120921 93.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11371 0 230 74 11675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013312002
X-RAY DIFFRACTIONf_angle_d1.285716377
X-RAY DIFFRACTIONf_chiral_restr0.06161839
X-RAY DIFFRACTIONf_plane_restr0.00922085
X-RAY DIFFRACTIONf_dihedral_angle_d21.82844431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.35091460.32442968X-RAY DIFFRACTION73.39
2.13-2.150.36511550.32113053X-RAY DIFFRACTION75.04
2.15-2.180.33841530.31773090X-RAY DIFFRACTION75.38
2.18-2.20.35861840.31553019X-RAY DIFFRACTION74.94
2.2-2.230.34391760.30093072X-RAY DIFFRACTION76.73
2.23-2.260.36481700.29893135X-RAY DIFFRACTION77.29
2.26-2.30.32461790.3033236X-RAY DIFFRACTION78.42
2.3-2.330.32661810.30153304X-RAY DIFFRACTION82.68
2.33-2.370.37751580.29393701X-RAY DIFFRACTION89.6
2.37-2.410.32912170.28543789X-RAY DIFFRACTION93.86
2.41-2.450.34712080.28434048X-RAY DIFFRACTION99.09
2.45-2.490.3212000.28364105X-RAY DIFFRACTION99.98
2.49-2.540.31012020.27394090X-RAY DIFFRACTION100
2.54-2.590.30162310.25614066X-RAY DIFFRACTION100
2.59-2.650.30392350.24854051X-RAY DIFFRACTION100
2.65-2.710.27841950.24944119X-RAY DIFFRACTION100
2.71-2.780.29571960.24554098X-RAY DIFFRACTION100
2.78-2.850.27872230.23884072X-RAY DIFFRACTION100
2.85-2.930.27452420.22684062X-RAY DIFFRACTION99.98
2.93-3.030.24482220.22644109X-RAY DIFFRACTION100
3.03-3.140.27731840.2314117X-RAY DIFFRACTION100
3.14-3.260.24631980.22274116X-RAY DIFFRACTION100
3.26-3.410.26512030.22054159X-RAY DIFFRACTION100
3.41-3.590.25422160.19874126X-RAY DIFFRACTION100
3.59-3.810.20432420.17484106X-RAY DIFFRACTION100
3.81-4.10.22062180.15734135X-RAY DIFFRACTION100
4.1-4.510.17082680.14014126X-RAY DIFFRACTION100
4.51-5.160.16592360.13054162X-RAY DIFFRACTION99.98
5.16-6.460.19272180.15034241X-RAY DIFFRACTION100
6.46-20.520.19412380.15254352X-RAY DIFFRACTION99.2

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