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- EMDB-10141: The structure of human thyroglobulin -

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Basic information

Database: EMDB / ID: EMD-10141
TitleThe structure of human thyroglobulin
Map data
Samplehuman thyroglobulin:
Thyroglobulin / ligand
Function / homology
Function and homology information

iodide transport / hormone biosynthetic process / thyroid hormone generation / regulation of myelination / thyroid gland development / hormone activity / signal transduction / extracellular space / extracellular region / identical protein binding
Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Carboxylesterase, type B / Tyrosine-protein kinase ephrin type A/B receptor-like / Thyroglobulin / Carboxylesterase type B, conserved site / Alpha/Beta hydrolase fold
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsCoscia F / Turk D / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)U105184326 to JL United Kingdom
Wellcome Trust202754/Z/16/Z to JL United Kingdom
CitationJournal: 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.
Validation ReportSummary, Full report, XML, About validation report
DepositionJul 24, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseFeb 12, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6scj
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
Supplemental images

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FileDownload / File: emd_10141.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 417.2 Å
1.04 Å/pix.
x 400 pix.
= 417.2 Å
1.04 Å/pix.
x 400 pix.
= 417.2 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.043 Å
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.09003922 - 0.1956845
Average (Standard dev.)0.00023077495 (±0.00327456)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 417.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0431.0431.043
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z417.200417.200417.200
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0900.1960.000

Supplemental data

Additional map: #1

Projections & Slices


Slices (1/2)
Density Histograms

Additional map: #2

Projections & Slices


Slices (1/2)
Density Histograms

Sample components

Entire human thyroglobulin

EntireName: human thyroglobulin / Details: dimeric / Number of components: 3

Component #1: protein, human thyroglobulin

ProteinName: human thyroglobulin / Details: dimeric / Recombinant expression: No
MassExperimental: 660 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

Component #2: protein, Thyroglobulin

ProteinName: Thyroglobulin / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 305.069844 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

Component #3: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 30 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.05 mg/mL / Buffer solution: TRIS 0.05M, 0.2M NaCl pH 8 / pH: 8
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 151601
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

Atomic model buiding

Output model

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