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- EMDB-14145: Structure of Native, iodinated bovine thyroglobulin solved on str... -

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Basic information

Entry
Database: EMDB / ID: EMD-14145
TitleStructure of Native, iodinated bovine thyroglobulin solved on strepavidin affinity grids.
Map dataMain map. This is a composit map build from a C2 map and two C1 map corresponding to both asymmetric units.
Sample
  • Complex: Native bovine thyroglobulin from thyroid gland, containing T3/T4 hormone precursors in two homonogenic sites.
    • Protein or peptide: Thyroglobulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsThyroglobulin / thyroid hormone / iodine / precursor / HORMONE
Function / homology
Function and homology information


hormone biosynthetic process / thyroid hormone generation / hormone activity / histone binding / extracellular space
Similarity search - Function
Thyroglobulin / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Putative ephrin-receptor like ...Thyroglobulin / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / Tyrosine-protein kinase ephrin type A/B receptor-like / Tyrosine-protein kinase ephrin type A/B receptor-like / Putative ephrin-receptor like / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Growth factor receptor cysteine-rich domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMarechal N / Weitz JC / Serrano BP / Zhang X
Funding support United States, 1 items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nat Commun / Year: 2022
Title: Formation of thyroid hormone revealed by a cryo-EM structure of native bovine thyroglobulin.
Authors: Nils Marechal / Banyuhay P Serrano / Xinyan Zhang / Charles J Weitz /
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 ...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.
History
DepositionJan 15, 2022-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14145.png

Downloads & links

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Map

FileDownload / File: emd_14145.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map. This is a composit map build from a C2 map and two C1 map corresponding to both asymmetric units.
Voxel sizeX=Y=Z: 0.825 Å
Density
Contour LevelBy AUTHOR: 6.0
Minimum - Maximum-46.450512000000003 - 70.826995999999994
Average (Standard dev.)-0.013722293 (±1.0308435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Density modified map for the single asymmetric unit processing

Fileemd_14145_additional_1.map
AnnotationDensity modified map for the single asymmetric unit processing
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native bovine thyroglobulin from thyroid gland, containing T3/T4 ...

EntireName: Native bovine thyroglobulin from thyroid gland, containing T3/T4 hormone precursors in two homonogenic sites.
Components
  • Complex: Native bovine thyroglobulin from thyroid gland, containing T3/T4 hormone precursors in two homonogenic sites.
    • Protein or peptide: Thyroglobulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Native bovine thyroglobulin from thyroid gland, containing T3/T4 ...

SupramoleculeName: Native bovine thyroglobulin from thyroid gland, containing T3/T4 hormone precursors in two homonogenic sites.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle) / Organ: thyroid gland
Molecular weightTheoretical: 670 KDa

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Macromolecule #1: Thyroglobulin

MacromoleculeName: Thyroglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle) / Organ: thyroid gland
Molecular weightTheoretical: 304.042562 KDa
SequenceString: MALALWVFGL LDLICLASAN IFEYQVDAQP LRPCELQRER AFLKREDYVP QCAEDGSFQT VQCGKDGASC WCVDADGREV PGSRQPGRP AACLSFCQLQ KQQILLSSYI NSTATSYLPQ CQDSGDYSPV QCDLRRRQCW CVDAEGMEVY GTRQQGRPAR C PRSCEIRN ...String:
MALALWVFGL LDLICLASAN IFEYQVDAQP LRPCELQRER AFLKREDYVP QCAEDGSFQT VQCGKDGASC WCVDADGREV PGSRQPGRP AACLSFCQLQ KQQILLSSYI NSTATSYLPQ CQDSGDYSPV QCDLRRRQCW CVDAEGMEVY GTRQQGRPAR C PRSCEIRN RRLLHGVGDR SPPQCSPDGA FRPVQCKFVN TTDMMIFDLV HSYSRFPDAF VTFSSFRSRF PEVSGYCYCA DS QGRELAE TGLELLLDEI YDTIFAGLDL ASTFAETTLY RILQRRFLAV QLVISGRFRC PTKCEVERFA ATSFRHPYVP SCH PDGEYQ AAQCQQGGPC WCVDSRGQEI PGTRQRGEPP SCAEDQSCPS ERRRAFSRLR FGPSGYFSRR SLLLAPEEGP VSQR FARFT ASCPPSIKEL FLDSGIFQPM LQGRDTRFVA PESLKEAIRG LFPSRELARL ALQFTTNAKR LQQNLFGGRF LVKVG QFNL SGALGTRGTF NFSHFFQQLG LPGFQDGRAL ADLAKPLSVG LNSNPASEAP KASKIDVALR KPVVGSFGFE VNLQEN QNA LQFLSSFLEL PEFLLFLQHA ISVPEDIARD LGDVMEMVFS SQGCGQAPGS LFVPACTAEG SYEEVQCFAG DCWCVDA QG RELAGSRVRG GRPRCPTECE KQRARMQSLL GSQPAGSSLF VPACTSKGNF LPVQCFNSEC YCVDTEGQPI PGTRSALG E PKKCPSPCQL QAERAFLGTV RTLVSNPSTL PALSSIYIPQ CSASGQWSPV QCDGPPEQAF EWYERWEAQN SAGQALTPA ELLMKIMSYR EAASRNFRLF IQNLYEAGQQ GIFPGLARYS SFQDVPVSVL EGNQTQPGGN VFLEPYLFWQ ILNGQLDRYP GPYSDFSAP LAHFDLRSCW CVDEAGQKLE GTRNEPNKVP ACPGSCEEVK LRVLQFIREA EEIVTYSNSS RFPLGESFLA A KGIRLTDE ELAFPPLSPS RETFLEKFLS GSDYAIRLAA QSTFDFYQRR LVTLAESPRA PSPVWSSAYL PQCDAFGGWE PV QCHAATG HCWCVDGKGE YVPTSLTARS RQIPQCPTSC ERLRASGLLS SWKQAGVQAE PSPKDLFIPT CLETGEFARL QAS EAGTWC VDPASGEGVP PGTNSSAQCP SLCEVLQSGV PSRRTSPGYS PACRAEDGGF SPVQCDPAQG SCWCVLGSGE EVPG TRVAG SQPACESPQC PLPFSVADVA GGAILCERAS GLGAAAGQRC QLRCSQGYRS AFPPEPLLCS VQRRRWESRP PQPRA CQRP QFWQTLQTQA QFQLLLPLGK VCSADYSGLL LAFQVFLLDE LTARGFCQIQ VKTAGTPVSI PVCDDSSVKV ECLSRE RLG VNITWKLQLV DAPPASLPDL QDVEEALAGK YLAGRFADLI QSGTFQLHLD SKTFSADTSI RFLQGDRFGT SPRTQFG CL EGFGRVVAAS DASQDALGCV KCPEGSYFQD EQCIPCPAGF YQEQAGSLAC VPCPEGRTTV YAGAFSQTHC VTDCQKNE V GLQCDQDSQY RASQRDRTSG KAFCVDGEGR RLPWTEAEAP LVDAQCLVMR KFEKLPESKV IFSADVAVMV RSEVPGSES SLMQCLADCA LDEACGFLTV STAGSEVSCD FYAWASDSIA CTTSGRSEDA LGTSQATSFG SLQCQVKVRS REGDPLAVYL KKGQEFTIT GQKRFEQTGF QSALSGMYSP VTFSASGASL AEVHLFCLLA CDHDSCCDGF ILVQVQGGPL LCGLLSSPDV L LCHVRDWR DPAEAQANAS CPGVTYDQDS RQVTLRLGGQ EIRGLTPLEG TQDTLTSFQQ VYLWKDSDMG SRSESMGCRR DT EPRPASP SETDLTTGLF SPVDLIQVIV DGNVSLPSQQ HWLFKHLFSL QQANLWCLSR CAGEPSFCQL AEVTDSEPLY FTC TLYPEA QVCDDILESS PKGCRLILPR RPSALYRKKV VLQDRVKNFY NRLPFQKLTG ISIRNKVPMS DKSISSGFFE CERL CDMDP CCTGFGFLNV SQLKGGEVTC LTLNSLGLQT CSEEYGGVWR ILDCGSPDTE VRTYPFGWYQ KPVSPSDAPS FCPSV ALPA LTENVALDSW QSLALSSVIV DPSIRNFDVA HISTAAVGNF SAARDRCLWE CSRHQDCLVT TLQTQPGAVR CMFYAD TQS CTHSLQAQNC RLLLHEEATY IYRKPNIPLP GFGTSSPSVP IATHGQLLGR SQAIQVGTSW KPVDQFLGVP YAAPPLG EK RFRAPEHLNW TGSWEATKPR ARCWQPGIRT PTPPGVSEDC LYLNVFVPQN MAPNASVLVF FHNAAEGKGS GDRPAVDG S FLAAVGNLIV VTASYRTGIF GFLSSGSSEL SGNWGLLDQV VALTWVQTHI QAFGGDPRRV TLAADRGGAD IASIHLVTT RAANSRLFRR AVLMGGSALS PAAVIRPERA RQQAAALAKE VGCPSSSVQE MVSCLRQEPA RILNDAQTKL LAVSGPFHYW GPVVDGQYL RETPARVLQR APRVKVDLLI GSSQDDGLIN RAKAVKQFEE SQGRTSSKTA F(DHA)QALQNSLG GEAADAG VQ AAATWYYSLE HDSDD(T44)ASFS RALEQATRDY FIICPVIDMA SHWARTVRGN VFMYHAPESY SHSSLELLTD VLYA FGLPF YPAYEGQFTL EEKSLSLKIM QYFSNFIRSG NPNYPHEFSR RAPEFAAPWP DFVPRDGAES YKELSVLLPN RQGLK KADC SFWSKYIQSL KASADETKDG PSADSEEEDQ PAGSGLTEDL LGLPELASKT YSK

UniProtKB: Thyroglobulin

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 12 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 4
Details: Streaptavidin 2D crystal supported by a biotinylated monolayer, stabilized by thin carbon evaporation on lipid tails
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 34597 / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 2)) / Number images used: 242813
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3.1), cryoSPARC (ver. 2))
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7qtq:
Structure of Native, iodinated bovine thyroglobulin solved on strepavidin affinity grids.

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