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Yorodumi- PDB-8dqk: Intermediate resolution structure of barley (1,3;1,4)-beta-glucan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dqk | ||||||
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Title | Intermediate resolution structure of barley (1,3;1,4)-beta-glucan synthase CslF6. | ||||||
Components | Cellulose synthase-like CslF6 | ||||||
Keywords | TRANSFERASE / glucan / glycosyltransferase / cellulose / barley | ||||||
Function / homology | plant-type cell wall organization or biogenesis / Cellulose synthase / Cellulose synthase / cellulose synthase (UDP-forming) activity / cellulose biosynthetic process / Nucleotide-diphospho-sugar transferases / membrane / CslF6 Function and homology information | ||||||
Biological species | Hordeum vulgare (barley) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Ho, R. / Purushotham, P. / Zimmer, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Adv / Year: 2022 Title: Mechanism of mixed-linkage glucan biosynthesis by barley cellulose synthase-like CslF6 (1,3;1,4)-β-glucan synthase. Authors: Pallinti Purushotham / Ruoya Ho / Long Yu / Geoffrey B Fincher / Vincent Bulone / Jochen Zimmer / Abstract: Mixed-linkage (1,3;1,4)-β-glucans, which are widely distributed in cell walls of the grasses, are linear glucose polymers containing predominantly (1,4)-β-linked glucosyl units interspersed with ...Mixed-linkage (1,3;1,4)-β-glucans, which are widely distributed in cell walls of the grasses, are linear glucose polymers containing predominantly (1,4)-β-linked glucosyl units interspersed with single (1,3)-β-linked glucosyl units. Their distribution in cereal grains and unique structures are important determinants of dietary fibers that are beneficial to human health. We demonstrate that the barley cellulose synthase-like CslF6 enzyme is sufficient to synthesize a high-molecular weight (1,3;1,4)-β-glucan in vitro. Biochemical and cryo-electron microscopy analyses suggest that CslF6 functions as a monomer. A conserved "switch motif" at the entrance of the enzyme's transmembrane channel is critical to generate (1,3)-linkages. There, a single-point mutation markedly reduces (1,3)-linkage formation, resulting in the synthesis of cellulosic polysaccharides. Our results suggest that CslF6 monitors the orientation of the nascent polysaccharide's second or third glucosyl unit. Register-dependent interactions with these glucosyl residues reposition the polymer's terminal glucosyl unit to form either a (1,3)- or (1,4)-β-linkage. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dqk.cif.gz | 142.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dqk.ent.gz | 109.8 KB | Display | PDB format |
PDBx/mmJSON format | 8dqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8dqk_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8dqk_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8dqk_validation.xml.gz | 33.7 KB | Display | |
Data in CIF | 8dqk_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/8dqk ftp://data.pdbj.org/pub/pdb/validation_reports/dq/8dqk | HTTPS FTP |
-Related structure data
Related structure data | 27655MC 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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-Components
#1: Protein | Mass: 105193.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Gene: CslF6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: B1P2T4 |
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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: Barley cellulose synthase-like F6 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Hordeum vulgare (barley) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80347 / Symmetry type: POINT |