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- PDB-7spa: Chlorella virus Hyaluronan Synthase in the GlcNAc-primed, channel... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7spa | ||||||
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Title | Chlorella virus Hyaluronan Synthase in the GlcNAc-primed, channel-open state | ||||||
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![]() | MEMBRANE PROTEIN / glycosyltransferase / hyaluronan | ||||||
Function / homology | ![]() hyaluronan synthase activity / extracellular matrix assembly / hyaluronan biosynthetic process / extracellular polysaccharide biosynthetic process / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
![]() | Maloney, F.P. / Kuklewicz, J. / Zimmer, J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure, substrate recognition and initiation of hyaluronan synthase. Authors: Finn P Maloney / Jeremi Kuklewicz / Robin A Corey / Yunchen Bi / Ruoya Ho / Lukasz Mateusiak / Els Pardon / Jan Steyaert / Phillip J Stansfeld / Jochen Zimmer / ![]() ![]() ![]() ![]() Abstract: Hyaluronan is an acidic heteropolysaccharide comprising alternating N-acetylglucosamine and glucuronic acid sugars that is ubiquitously expressed in the vertebrate extracellular matrix. The high- ...Hyaluronan is an acidic heteropolysaccharide comprising alternating N-acetylglucosamine and glucuronic acid sugars that is ubiquitously expressed in the vertebrate extracellular matrix. The high-molecular-mass polymer modulates essential physiological processes in health and disease, including cell differentiation, tissue homeostasis and angiogenesis. Hyaluronan is synthesized by a membrane-embedded processive glycosyltransferase, hyaluronan synthase (HAS), which catalyses the synthesis and membrane translocation of hyaluronan from uridine diphosphate-activated precursors. Here we describe five cryo-electron microscopy structures of a viral HAS homologue at different states during substrate binding and initiation of polymer synthesis. Combined with biochemical analyses and molecular dynamics simulations, our data reveal how HAS selects its substrates, hydrolyses the first substrate to prime the synthesis reaction, opens a hyaluronan-conducting transmembrane channel, ensures alternating substrate polymerization and coordinates hyaluronan inside its transmembrane pore. Our research suggests a detailed model for the formation of an acidic extracellular heteropolysaccharide and provides insights into the biosynthesis of one of the most abundant and essential glycosaminoglycans in the human body. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 163.1 KB | Display | ![]() |
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PDB format | ![]() | 128 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 25370MC ![]() 7sp6C ![]() 7sp7C ![]() 7sp8C ![]() 7sp9C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data size: 2.3 TB Data #1: Unaligned movies of Chlorella virus hyaluronan synthase [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Antibody , 2 types, 2 molecules BC
#1: Antibody | Mass: 14783.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 15265.755 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein | Mass: 65336.484 Da / Num. of mol.: 1 / Mutation: D302N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CZ-2_118R, PBCVCZ2_118R / Plasmid: pET28a / Production host: ![]() ![]() |
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#4: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 2 molecules ![](data/chem/img/Y01.gif)
![](data/chem/img/3PE.gif)
![](data/chem/img/3PE.gif)
#5: Chemical | ChemComp-Y01 / |
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#6: Chemical | ChemComp-3PE / |
-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 |
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Sample preparation
Component | Name: Hyaluronan synthase in nanodiscs in complex with two camelid nanobodies. Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.0958 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Details: Sample incubated on grid 30s before blotting. Blot 4 seconds with force 4. Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8218 / Details: 40-frame movies were collected |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV |
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Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4391341 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 104995 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.26 Å2 | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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