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Yorodumi- PDB-8snc: Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8snc | |||||||||
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Title | Chlorella virus Hyaluronan Synthase bound to GlcA extended GlcNAc primer | |||||||||
Components |
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Keywords | TRANSFERASE / hyaluronic acid / hyaluronan / HA / HAS / glycosyltransferase / GT / membrane protein / nanobody / n-acetylglucosamine / glucuronic acid | |||||||||
Function / homology | Function and homology information hyaluronan synthase activity / extracellular matrix assembly / hyaluronan biosynthetic process / extracellular polysaccharide biosynthetic process / membrane Similarity search - Function | |||||||||
Biological species | Paramecium bursaria Chlorella virus CZ-2 Lama glama (llama) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Stephens, Z. / Zimmer, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Molecular insights into hyaluronan synthesis, secretion, and length control Authors: Gorniak, I. / Stephens, Z. / Erramilli, S.K. / Gawda, T. / Kossiakoff, A.A. / Zimmer, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8snc.cif.gz | 163.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8snc.ent.gz | 123.4 KB | Display | PDB format |
PDBx/mmJSON format | 8snc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8snc_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8snc_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8snc_validation.xml.gz | 33.1 KB | Display | |
Data in CIF | 8snc_validation.cif.gz | 46.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/8snc ftp://data.pdbj.org/pub/pdb/validation_reports/sn/8snc | HTTPS FTP |
-Related structure data
Related structure data | 40622MC 8sndC 8sneC 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
-Antibody , 2 types, 2 molecules BC
#2: Antibody | Mass: 14783.248 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli K-12 (bacteria) |
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#3: Antibody | Mass: 15184.657 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli K-12 (bacteria) |
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 65890.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Paramecium bursaria Chlorella virus CZ-2 Gene: CZ-2_118R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1H2Q1 |
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#4: Polysaccharide | beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 4 molecules
#5: Chemical | ChemComp-Y01 / | ||
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#6: Chemical | #7: Water | ChemComp-HOH / | |
-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: Ternary complex of Chlorella virus hyaluronan synthase bound to nanobodies 872 and 886 Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 95.3 kDa/nm / Experimental value: NO |
Source (natural) | Organism: Paramecium bursaria Chlorella virus 1 |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115974 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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