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- EMDB-24181: The structure of bovine thyroglobulin with iodinated tyrosines -

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Basic information

Entry
Database: EMDB / ID: EMD-24181
TitleThe structure of bovine thyroglobulin with iodinated tyrosines
Map dataCombined EM map of reconstructions from focused refinements around the region surrounding half of the dimeric Tg molecule and the arm region of a Tg monomer - resampled in finer grid points.
Sample
  • Complex: Bovine thyroglobulin purified from bovine thyroid
    • Protein or peptide: Thyroglobulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsthyroid hormone synthesis / HORMONE
Function / homology
Function and homology information


iodide transport / hormone biosynthetic process / thyroid hormone generation / regulation of myelination / thyroid gland development / hormone activity / extracellular space / identical protein binding
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 / Carboxylesterase type B, conserved site ...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 / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesBos indicus x Bos taurus (hybrid cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.61 Å
AuthorsKim K / Clarke OB
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: 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
DepositionJun 4, 2021-
Header (metadata) releaseNov 10, 2021-
Map releaseNov 10, 2021-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n4y
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24181.png

Downloads & links

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Map

FileDownload / File: emd_24181.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCombined EM map of reconstructions from focused refinements around the region surrounding half of the dimeric Tg molecule and the arm region of a Tg monomer - resampled in finer grid points.
Voxel sizeX=Y=Z: 0.7453 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.035
Minimum - Maximum-0.0070776534 - 0.32060194
Average (Standard dev.)0.0028776657 (±0.0057799513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 381.5936 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.745300781250.745300781250.74530078125
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z381.594381.594381.594
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0070.3210.003

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Supplemental data

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Mask #1

Fileemd_24181_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram (log scale)

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Mask #2

Fileemd_24181_msk_2.map
Projections & Slices
AxesZYX

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Additional map: EM map of the focused refinement on the arm region of a Tg monomer

Fileemd_24181_additional_1.map
AnnotationEM map of the focused refinement on the arm region of a Tg monomer
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Combined EM map of density-modified maps of focused...

Fileemd_24181_additional_10.map
AnnotationCombined EM map of density-modified maps of focused refinements around the region surrounding half of the dimeric Tg molecule and the arm region of a Tg monomer - the model is aligned to this map
Projections & Slices
AxesZYX

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Histogram

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Additional map: EM map of the global consensus refinement -...

Fileemd_24181_additional_2.map
AnnotationEM map of the global consensus refinement - the reference map for subsequent focused refinements
Projections & Slices
AxesZYX

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Histogram

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Additional map: EM map of the focused refinement on the...

Fileemd_24181_additional_3.map
AnnotationEM map of the focused refinement on the region surrounding half of the dimeric Tg molecule
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Additional map: The second EM half map of the focused...

Fileemd_24181_additional_4.map
AnnotationThe second EM half map of the focused refinement on the region surrounding half of the dimeric Tg molecule
Projections & Slices
AxesZYX

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Histogram

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Additional map: The first EM half map of the focused...

Fileemd_24181_additional_5.map
AnnotationThe first EM half map of the focused refinement on the region surrounding half of the dimeric Tg molecule
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: The second EM half map of the focused...

Fileemd_24181_additional_6.map
AnnotationThe second EM half map of the focused refinement on the arm region of a Tg monomer
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: The first EM half map of the focused...

Fileemd_24181_additional_7.map
AnnotationThe first EM half map of the focused refinement on the arm region of a Tg monomer
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: density-modified EM map of the focused refinement on...

Fileemd_24181_additional_8.map
Annotationdensity-modified EM map of the focused refinement on the arm region of a Tg monomer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: density-modified EM map of the focused refinement on...

Fileemd_24181_additional_9.map
Annotationdensity-modified EM map of the focused refinement on the region surrounding half of the dimeric Tg molecule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The first EM half map of the global consensus reconstruction

Fileemd_24181_half_map_1.map
AnnotationThe first EM half map of the global consensus reconstruction
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: The second EM half map of the global consensus reconstruction

Fileemd_24181_half_map_2.map
AnnotationThe second EM half map of the global consensus reconstruction
Projections & Slices
AxesZYX

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Sample components

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Entire : Bovine thyroglobulin purified from bovine thyroid

EntireName: Bovine thyroglobulin purified from bovine thyroid
Components
  • Complex: Bovine thyroglobulin purified from bovine thyroid
    • Protein or peptide: Thyroglobulin
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Bovine thyroglobulin purified from bovine thyroid

SupramoleculeName: Bovine thyroglobulin purified from bovine thyroid / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos indicus x Bos taurus (hybrid cattle)
Molecular weightTheoretical: 660 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 indicus x Bos taurus (hybrid cattle)
Molecular weightTheoretical: 303.087844 KDa
SequenceString: NIFE(T44)QVDAQ PLRPCELQRE RAFLKREDYV PQCAEDGSFQ TVQCGKDGAS CWCVDADGRE VPGSRQPGRP AACLSF CQL QKQQILLSSY INSTATSYLP QCQDSGDYSP VQCDLRRRQC WCVDAEGMEV YGTRQQGRPA RCPRSCEIRN RRLLHGV GD RSPPQCSPDG ...String:
NIFE(T44)QVDAQ PLRPCELQRE RAFLKREDYV PQCAEDGSFQ TVQCGKDGAS CWCVDADGRE VPGSRQPGRP AACLSF CQL QKQQILLSSY INSTATSYLP QCQDSGDYSP VQCDLRRRQC WCVDAEGMEV YGTRQQGRPA RCPRSCEIRN RRLLHGV GD RSPPQCSPDG AFRPVQCKFV NTTDMMIFDL VHSYSRFPDA FVTFSSFRSR FPEVSGYCYC ADSQGRELAE TGLELLLD E IYDTIFAGLD LASTFAETTL YRILQRRFLA VQLVISGRFR CPTKCEVERF AATSFRHPYV PSCHPDGEYQ AAQCQQGGP CWCVDSRGQE IPGTRQRGEP PSCAEDQSCP SERRRAFSRL RFGPSGYFSR RSLLLAPEEG PVSQRFARFT ASCPPSIKEL FLDSGIFQP MLQGRDTRFV APESLLKEAI RGLFPSRELA RLALQFTTNA KRLQQNLFGG RFLVNVGQFN LSGALGTRGT F NFSHFFQQ LGLPGFQDGR ALADLAKPLS VGLNSNPASE APKASKIDVA LRKPVVGSFG FEVNLQENQN ALQFLSSFLE LP EFLLFLQ HAISVPEDIA RDLGDVMEMV FSSQGCGQAP GSLFVPACTA EGSYEEVQCF AGDCWCVDAQ GRELAGSRVR GGR PRCPTE CEKQRARMQS LLGSQPAGSS LFVPACTSKG NFLPVQCFNS ECYCVDTEGQ PIPGTRSALG EPKKCPSPCQ LQAE RAFLG TVRTLVSNPS TLPALSSIYI PQCSASGQWS PVQCDGPPEQ AFEWYERWEA QNSAGQALTP AELLMKIMSY REAAS RNFR LFIQNLYEAG QQGIFPGLAR YSSFQDVPVS VLEGNQTQPG GNVFLEPYLF WQILNGQLDR YPGPYSDFSA PLAHFD LRS CWCVDEAGQK LEGTRNEPNK VPACPGSCEE VKLRVLQFIR EAEEIVTYSN SSRFPLGESF LAAKGIRLTD EELAFPP LS PSRETFLEKF LSGSDYAIRL AAQSTFDFYQ RRLVTLAESP RAPSPVWSSA YLPQCDAFGG WEPVQCHAAT GHCWCVDG K GEYVPTSLTA RSRQIPQCPT SCERLRASGL LSSWKQAGVQ AEPSPKDLFI PTCLETGEFA RLQASEAGTW CVDPASGEG VPPGTNSSAQ CPSLCEVLQS GVPSRRTSPG YSPACRAEDG GFSPVQCDPA QGSCWCVLGS GEEVPGTRVA GSQPACESPQ CPLPFSVAD VAGGAILCER ASGLGAAAGQ RCQLRCSQGY RSAFPPEPLL CSVQRRRWES RPPQPRACQR PQFWQTLQTQ A QFQLLLPL GKVCSADYSG LLLAFQVFLL DELTARGFCQ IQVKTAGTPV SIPVCDDSSV KVECLSRERL GVNITWKLQL VD APPASLP DLQDVEEALA GKYLAGRFAD LIQSGTFQLH LDSKTFSADT SIRFLQGDRF GISPRTQFGC LEGFGRVVAA SDA SQDALG CVKCPEGSYF QDEQCIPCPA GFYQEQAGSL ACVPCPEGRT TVYAGAFSQT HCVTDCQKNE VGLQCDQDGQ YRAS QRDRT SGKAFCVDGE GRRLPWTEAE APLVDAQCLV MRKFEKLPES KVIFSADVAV MVRSEVPGSE SSLMQCLADC ALDEA CGFL TVSTAGSEVS CDFYAWASDS IACTTSGRSE DALGTSQATS FGSLQCQVKV RSREGDPLAV YLKKGQEFTI TGQKRF EQT GFQSALSGMY SPVTFSASGA SLAEVHLFCL LACDHDSCCD GFILVQVQGG PLLCGLLSSP DVLLCHVRDW RDPAEAQ AN ASCPGVTYDQ DSRQVTLRLG GQEIRGLTPL EGTQDTLTSF QQVYLWKDSD MGSRSESMGC RRDTEPRPAS PSETDLTT G LFSPVDLIQV IVDGNVSLPS QQHWLFKHLF SLQQANLWCL SRCAGEPSFC QLAEVTDSEP LYFTCTLYPE AQVCDDILE SSPKGCRLIL PRRPSALYRK KVVLQDRVKN FYNRLPFQKL TGISIRNKVP MSDKSISSGF FECERLCDMD PCCTGFGFLN VSQLKGGEV TCLTLNSLGL QTCSEE(TYI)GGV WRILDCGSPD TEVRTYPFGW YQKPVSPSDA PSFCPSVALP ALTENVA LD SWQSLALSSV IVDPSIRNFD VAHISTAAVG NFSAARDRCL WECSRHQDCL VTTLQTQPGA VRCMFYADTQ SCTHSLQA Q NCRLLLHEEA TYIYRKPNIP LPGFGTSSPS VPIATHGQLL GRSQAIQVGT SWKPVDQFLG VPYAAPPLGE KRFRAPEHL NWTGSWEATK PRARCWQPGI RTPTPPGVSE DCLYLNVFVP QNMPPNASVL VFFHNAAEGK GSGDRPAVDG SFLAAVGNLI VVTASYRTG IFGFLSSGSS ELSGNWGLLD QVVALTWVQT HIQAFGGDPR RVTLAADRGG ADIASIHLVT TRAANSRLFR R AVLMGGSA LSPAAVIRPE RARQQAAALA KEVGCPSSSV QEMVSCLRQE PARILNDAQT KLLAVSGPFH YWGPVVDGQY LR ETPARVL QRAPRVKVDL LIGSSQDDGL INRAKAVKQF EESQGRTSSK TAFYQALQNS LGGEAADAGV QAAATWYYSL EHD SDD(T44)AS FSRALEQATR DYFIICPVID MASHWARTVR GNVFMYHAPE SYSHSSLELL TDVLYAFGLP FYPAYEGQFT LEEKSLSLK IMQYFSNFIR SGNPNYPHEF SRRAPEFAAP WPDFVPRDGA ESYKELSVLL PNRQGLKKAD CSFWSKYIQS L KASADETK DGPSADSEEE DQPAGSGLTE DLLGLPELAS KTYSK

UniProtKB: Thyroglobulin

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 308 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 71.32 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 554053
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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