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- PDB-7aua: Cryo-EM structure of human exostosin-like 3 (EXTL3) in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7aua | |||||||||||||||||||||||||||
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Title | Cryo-EM structure of human exostosin-like 3 (EXTL3) in complex with UDP | |||||||||||||||||||||||||||
![]() | Exostosin-like 3 | |||||||||||||||||||||||||||
![]() | TRANSFERASE / glycosyltransferase / heparan / n-acetylglucosaminyltransferase | |||||||||||||||||||||||||||
Function / homology | ![]() 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 | |||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å | |||||||||||||||||||||||||||
![]() | Wilson, L.F.L. / Dendooven, T. / Hardwick, S.W. / Chirgadze, D.Y. / Luisi, B.F. / Logan, D.T. / Mani, K. / Dupree, P. | |||||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: The structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis. Authors: L F L Wilson / T Dendooven / S W Hardwick / A Echevarría-Poza / T Tryfona / K B R M Krogh / D Y Chirgadze / B F Luisi / D T Logan / K Mani / P Dupree / ![]() ![]() ![]() ![]() Abstract: Heparan sulfate is a highly modified O-linked glycan that performs diverse physiological roles in animal tissues. Though quickly modified, it is initially synthesised as a polysaccharide of ...Heparan sulfate is a highly modified O-linked glycan that performs diverse physiological roles in animal tissues. Though quickly modified, it is initially synthesised as a polysaccharide of alternating β-D-glucuronosyl and N-acetyl-α-D-glucosaminyl residues by exostosins. These enzymes generally possess two glycosyltransferase domains (GT47 and GT64)-each thought to add one type of monosaccharide unit to the backbone. Although previous structures of murine exostosin-like 2 (EXTL2) provide insight into the GT64 domain, the rest of the bi-domain architecture is yet to be characterised; hence, how the two domains co-operate is unknown. Here, we report the structure of human exostosin-like 3 (EXTL3) in apo and UDP-bound forms. We explain the ineffectiveness of EXTL3's GT47 domain to transfer β-D-glucuronosyl units, and we observe that, in general, the bi-domain architecture would preclude a processive mechanism of backbone extension. We therefore propose that heparan sulfate backbone polymerisation occurs by a simple dissociative mechanism. | |||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 262.3 KB | Display | ![]() |
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PDB format | ![]() | 210.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 46.4 KB | Display | |
Data in CIF | ![]() | 70.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 11926MC ![]() 7au2C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 101705.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: O43909, glucuronosyl-galactosyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Chemical | #5: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Homodimer of EXTL3 globular domain / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.17 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 48.46 e/Å2 / Detector mode: INTEGRATING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1133069 | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238379 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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