7QTQ | pdb_00007qtq

Structure of Native, iodinated bovine thyroglobulin solved on strepavidin affinity grids.

PDB DOI: https://doi.org/10.2210/pdb7QTQ/pdb
EM Map EMD-14145: EMDB EMDataResource

Classification: HORMONE
Organism(s): Bos taurus
Mutation(s): Yes

Deposited: 2022-01-15 Released: 2022-05-04
Deposition Author(s): Marechal, N., Weitz, J.C., Serrano, B.P., Zhang, X.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Formation of thyroid hormone revealed by a cryo-EM structure of native bovine thyroglobulin.

Marechal, N., Serrano, B.P., Zhang, X., Weitz, C.J.

(2022) Nat Commun 13: 2380-2380

PubMed: 35501346 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-022-30082-4
Primary Citation Related Structures:
7QTQ

PubMed Abstract:
Thyroid hormones are essential regulators of metabolism, development, and growth. They are formed from pairs of iodinated tyrosine residues within the precursor thyroglobulin (TG), a 660-kDa homodimer of the thyroid gland, by an oxidative coupling reaction. Tyrosine pairs that give rise to thyroid hormones have been assigned within the structure of human TG, but the process of hormone formation is poorly understood. Here we report a ~3.3-Å cryo-EM structure of native bovine TG with nascent thyroid hormone formed at one of the predicted hormonogenic sites. Local structural rearrangements provide insight into mechanisms underlying thyroid hormone formation and stabilization.

Organizational Affiliation

Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA.

Macromolecule Content

Total Structure Weight: 612.76 kDa
Atom Count: 28,133
Modeled Residue Count: 3,579
Deposited Residue Count: 5,538
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thyroglobulin	A, B	2,769	Bos taurus	Mutation(s): 3
UniProt
Find proteins for P01267 (Bos taurus) Explore P01267 Go to UniProtKB: P01267
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01267
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, F [auth E]	3		N-Glycosylation	Interactions Focus chain C Focus chain F [auth E] Interactions & Density Focus chain C Focus chain F [auth E]
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E [auth F]	2		N-Glycosylation	Interactions Focus chain D Focus chain E [auth F] Interactions & Density Focus chain D Focus chain E [auth F]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DHA Query on DHA	A, B	PEPTIDE LINKING	C₃ H₅ N O₂		SER

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.30 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
RECONSTRUCTION	cryoSPARC	2
MODEL REFINEMENT	PHENIX	1.18.2
MODEL REFINEMENT	Coot

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-05-04

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded	United States	--

Revision History (Full details and data files)

Version 1.0: 2022-05-04
Type: Initial release
Version 1.1: 2022-05-18
Changes: Database references
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection, Derived calculations