+Open data
-Basic information
Entry | Database: PDB / ID: 7n4y | |||||||||
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Title | The structure of bovine thyroglobulin with iodinated tyrosines | |||||||||
Components | Thyroglobulin | |||||||||
Keywords | HORMONE / thyroid hormone synthesis | |||||||||
Function / homology | Function and homology information hormone biosynthetic process / iodide transport / thyroid hormone generation / regulation of myelination / thyroid gland development / hormone activity / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | Bos indicus x Bos taurus (hybrid cattle) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.61 Å | |||||||||
Authors | Kim, K. / Clarke, O.B. | |||||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: The structure of natively iodinated bovine thyroglobulin. Authors: Kookjoo Kim / Mykhailo Kopylov / Daija Bobe / Kotaro Kelley / Edward T Eng / Peter Arvan / Oliver B Clarke / Abstract: Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues ...Thyroglobulin is a homodimeric glycoprotein that is essential for the generation of thyroid hormones in vertebrates. Upon secretion into the lumen of follicles in the thyroid gland, tyrosine residues within the protein become iodinated to produce monoiodotyrosine (MIT) and diiodotyrosine (DIT). A subset of evolutionarily conserved pairs of DIT (and MIT) residues can then engage in oxidative coupling reactions that yield either thyroxine (T; produced from coupling of a DIT `acceptor' with a DIT `donor') or triiodothyronine (T; produced from coupling of a DIT acceptor with an MIT donor). Although multiple iodotyrosine residues have been identified as potential donors and acceptors, the specificity and structural context of the pairings (i.e. which donor is paired with which acceptor) have remained unclear. Here, single-particle cryogenic electron microscopy (cryoEM) was used to generate a high-resolution reconstruction of bovine thyroglobulin (2.3 Å resolution in the core region and 2.6 Å overall), allowing the structural characterization of two post-reaction acceptor-donor pairs as well as tyrosine residues modified as MIT and DIT. A substantial spatial separation between donor Tyr149 and acceptor Tyr24 was observed, suggesting that for thyroxine synthesis significant peptide motion is required for coupling at the evolutionarily conserved thyroglobulin amino-terminus. | |||||||||
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 | 7n4y.cif.gz | 856.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n4y.ent.gz | 685.7 KB | Display | PDB format |
PDBx/mmJSON format | 7n4y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n4y_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7n4y_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7n4y_validation.xml.gz | 131.7 KB | Display | |
Data in CIF | 7n4y_validation.cif.gz | 207.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/7n4y ftp://data.pdbj.org/pub/pdb/validation_reports/n4/7n4y | HTTPS FTP |
-Related structure data
Related structure data | 24181MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10833 (Title: The structure of natively iodinated bovine thyroglobulin Data size: 1.2 TB Data #1: Unaligned multi-frame micrographs of bovine thyroglobulin [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein / Non-polymers , 2 types, 310 molecules AB
#1: Protein | Mass: 303087.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos indicus x Bos taurus (hybrid cattle) / References: UniProt: A0A4W2CHS8 #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 18 molecules
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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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: Bovine thyroglobulin purified from bovine thyroid / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Molecular weight | Value: 0.66 MDa / Experimental value: YES |
Source (natural) | Organism: Bos indicus x Bos taurus (hybrid cattle) |
Buffer solution | pH: 7.4 |
Specimen | 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 R0.6/1 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS 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: 71.32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 554053 / Symmetry type: POINT | ||||||||||||||||||||||||
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