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Yorodumi- PDB-7scj: Cryo-EM structure of the human Exostosin-1 and Exostosin-2 hetero... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7scj | ||||||
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Title | Cryo-EM structure of the human Exostosin-1 and Exostosin-2 heterodimer in complex with a 4-sugar oligosaccharide acceptor analog | ||||||
Components |
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Keywords | TRANSFERASE / exostosin1 / exostosin2 / glycosyltransferase / heparan sulfate / acceptor | ||||||
Function / homology | Function and homology information glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase / hypersensitivity / heart field specification / lymphocyte adhesion to endothelial cell of high endothelial venule / heparan sulfate N-acetylglucosaminyltransferase activity / glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity / smoothened signaling pathway involved in lung development / developmental growth involved in morphogenesis ...glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase / hypersensitivity / heart field specification / lymphocyte adhesion to endothelial cell of high endothelial venule / heparan sulfate N-acetylglucosaminyltransferase activity / glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity / N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity / smoothened signaling pathway involved in lung development / developmental growth involved in morphogenesis / sweat gland development / perichondral bone morphogenesis / mesenchymal cell differentiation involved in bone development / response to leukemia inhibitory factor / UDP-N-acetylglucosamine transferase complex / chondroitin sulfate metabolic process / response to heparin / chondrocyte hypertrophy / embryonic skeletal joint development / hematopoietic stem cell migration to bone marrow / heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process / fluid transport / glucuronosyltransferase activity / limb joint morphogenesis / tight junction organization / heparin biosynthetic process / Defective EXT2 causes exostoses 2 / Defective EXT1 causes exostoses 1, TRPS2 and CHDS / stomach development / sebaceous gland development / glomerular basement membrane development / heparan sulfate proteoglycan biosynthetic process / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / lymphocyte migration into lymphoid organs / dendrite self-avoidance / hematopoietic stem cell homeostasis / chondrocyte proliferation / glandular epithelial cell differentiation / dendritic cell migration / endochondral bone morphogenesis / sulfation / endochondral bone growth / podocyte differentiation / sodium ion homeostasis / acetylglucosaminyltransferase activity / basement membrane organization / cartilage development involved in endochondral bone morphogenesis / polysaccharide biosynthetic process / cranial skeletal system development / vocalization behavior / stem cell division / olfactory bulb development / vacuole organization / multicellular organismal-level water homeostasis / leukocyte tethering or rolling / response to light intensity / endoderm development / endochondral ossification / fear response / regulation of tumor necrosis factor-mediated signaling pathway / protein N-linked glycosylation / cellular response to fibroblast growth factor stimulus / collagen fibril organization / neural crest cell differentiation / ossification involved in bone maturation / motor behavior / cell adhesion mediated by integrin / optic nerve development / hair follicle morphogenesis / epithelial tube branching involved in lung morphogenesis / cell fate commitment / heart contraction / BMP signaling pathway / glycosyltransferase activity / protein glycosylation / mesoderm development / antigen processing and presentation / social behavior / mesoderm formation / catalytic complex / hematopoietic stem cell differentiation / canonical Wnt signaling pathway / blood vessel remodeling / fibroblast growth factor receptor signaling pathway / chondrocyte differentiation / bone resorption / ossification / gastrulation / synaptic transmission, glutamatergic / axon guidance / regulation of blood pressure / wound healing / protein catabolic process / vasodilation / multicellular organism growth / cellular response to virus / gene expression / protein-containing complex assembly / protein heterodimerization activity Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||
Authors | Li, H. / Li, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Chem Biol / Year: 2023 Title: Structural basis for heparan sulfate co-polymerase action by the EXT1-2 complex. Authors: Hua Li / Digantkumar Chapla / Robert A Amos / Annapoorani Ramiah / Kelley W Moremen / Huilin Li / Abstract: Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-) co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix ...Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-) co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix proteins. In mammals, HS repeat units are extended by an obligate heterocomplex of two exostosin family members, EXT1 and EXT2, where each protein monomer contains distinct GT47 (GT-B fold) and GT64 (GT-A fold) glycosyltransferase domains. In this study, we generated human EXT1-EXT2 (EXT1-2) as a functional heterocomplex and determined its structure in the presence of bound donor and acceptor substrates. Structural data and enzyme activity of catalytic site mutants demonstrate that only two of the four glycosyltransferase domains are major contributors to co-polymer syntheses: the EXT1 GT-B fold β1,4GlcA transferase domain and the EXT2 GT-A fold α1,4GlcNAc transferase domain. The two catalytic sites are over 90 Å apart, indicating that HS is synthesized by a dissociative process that involves a single catalytic site on each monomer. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7scj.cif.gz | 220.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7scj.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 7scj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7scj_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7scj_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7scj_validation.xml.gz | 46.1 KB | Display | |
Data in CIF | 7scj_validation.cif.gz | 68.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/7scj ftp://data.pdbj.org/pub/pdb/validation_reports/sc/7scj | HTTPS FTP |
-Related structure data
Related structure data | 25036MC 7schC 7sckC 7uqxC 7uqyC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 83404.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXT1 / Production host: Mammalia (mammals) References: UniProt: Q16394, glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase, N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase |
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#2: Protein | Mass: 77180.984 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EXT2 / Production host: Mammalia (mammals) References: UniProt: Q93063, glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase, N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose Type: oligosaccharide / Mass: 600.525 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 2 molecules
#6: Chemical |
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-Details
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 |
-Sample preparation
Component | Name: hEXT1/2 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||
Source (recombinant) | Organism: Mammalia (mammals) | |||||||||||||||
Buffer solution | pH: 7 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 299 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 193 K / Temperature (min): 193 K / Residual tilt: 0.05 mradians |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3080 |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||
Particle selection | Num. of particles selected: 1938290 | ||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91157 / Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL |