+Open data
-Basic information
Entry | Database: PDB / ID: 6scj | |||||||||
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Title | The structure of human thyroglobulin | |||||||||
Components | Thyroglobulin | |||||||||
Keywords | HORMONE / Thyroglobulin / Thyroid / thyroid hormones / Tri-iodo-thyronine / Thyroxine | |||||||||
Function / homology | Function and homology information hormone biosynthetic process / iodide transport / thyroid hormone generation / regulation of myelination / thyroid gland development / hormone activity / signal transduction / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Coscia, F. / Turk, D. / Lowe, J. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nature / Year: 2020 Title: The structure of human thyroglobulin. Authors: Francesca Coscia / Ajda Taler-Verčič / Veronica T Chang / Ludwig Sinn / Francis J O'Reilly / Thierry Izoré / Miha Renko / Imre Berger / Juri Rappsilber / Dušan Turk / Jan Löwe / Abstract: Thyroglobulin (TG) is the protein precursor of thyroid hormones, which are essential for growth, development and the control of metabolism in vertebrates. Hormone synthesis from TG occurs in the ...Thyroglobulin (TG) is the protein precursor of thyroid hormones, which are essential for growth, development and the control of metabolism in vertebrates. Hormone synthesis from TG occurs in the thyroid gland via the iodination and coupling of pairs of tyrosines, and is completed by TG proteolysis. Tyrosine proximity within TG is thought to enable the coupling reaction but hormonogenic tyrosines have not been clearly identified, and the lack of a three-dimensional structure of TG has prevented mechanistic understanding. Here we present the structure of full-length human thyroglobulin at a resolution of approximately 3.5 Å, determined by cryo-electron microscopy. We identified all of the hormonogenic tyrosine pairs in the structure, and verified them using site-directed mutagenesis and in vitro hormone-production assays using human TG expressed in HEK293T cells. Our analysis revealed that the proximity, flexibility and solvent exposure of the tyrosines are the key characteristics of hormonogenic sites. We transferred the reaction sites from TG to an engineered tyrosine donor-acceptor pair in the unrelated bacterial maltose-binding protein (MBP), which yielded hormone production with an efficiency comparable to that of TG. Our study provides a framework to further understand the production and regulation of thyroid hormones. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6scj.cif.gz | 871.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6scj.ent.gz | 719.5 KB | Display | PDB format |
PDBx/mmJSON format | 6scj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6scj_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 6scj_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 6scj_validation.xml.gz | 133.7 KB | Display | |
Data in CIF | 6scj_validation.cif.gz | 206.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/6scj ftp://data.pdbj.org/pub/pdb/validation_reports/sc/6scj | HTTPS FTP |
-Related structure data
Related structure data | 10141MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10666 (Title: Human thyroglobulin / Data size: 1.7 TB Data #1: un-aligned frames for endogenous human thyroglobulin (eTG) on graphene oxide grids (Krios 300 kV, K2 camera) [micrographs - multiframe] Data #2: un-aligned frames for recombinant human thyroglobulin produced in HEK cells (rTG) on graphene oxide grids (Krios 300 kV, K2 camera) [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 305069.844 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TG / Cell line (production host): HEK / Production host: Homo sapiens (human) / Variant (production host): 293T / References: UniProt: P01266 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Sugar | ChemComp-NAG / 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: human thyroglobulin / Type: COMPLEX / Details: dimeric / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.660 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 / Details: TRIS 0.05M, 0.2M NaCl pH 8 |
Specimen | Conc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK III / 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 |
Image recording | Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: (1.14rc2_3191: phenix.real_space_refine) / Classification: refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 151601 / Symmetry type: POINT |