+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12073 | |||||||||
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Title | Cryo-EM Structure of Human Thyroglobulin | |||||||||
Map data | human Thyroglobulin, composite map | |||||||||
Sample |
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Keywords | Thyroglobulin / T3 and T4 Hormonogenesis / cryo-EM / HORMONE | |||||||||
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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Adaixo R / Righetto R | |||||||||
Funding support | Denmark, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of native human thyroglobulin. Authors: Ricardo Adaixo / Eva M Steiner / Ricardo D Righetto / Alexander Schmidt / Henning Stahlberg / Nicholas M I Taylor / Abstract: The thyroglobulin (TG) protein is essential to thyroid hormone synthesis, plays a vital role in the regulation of metabolism, development and growth and serves as intraglandular iodine storage. Its ...The thyroglobulin (TG) protein is essential to thyroid hormone synthesis, plays a vital role in the regulation of metabolism, development and growth and serves as intraglandular iodine storage. Its architecture is conserved among vertebrates. Synthesis of triiodothyronine (T) and thyroxine (T) hormones depends on the conformation, iodination and post-translational modification of TG. Although structural information is available on recombinant and deglycosylated endogenous human thyroglobulin (hTG) from patients with goiters, the structure of native, fully glycosylated hTG remained unknown. Here, we present the cryo-electron microscopy structure of native and fully glycosylated hTG from healthy thyroid glands to 3.2 Å resolution. The structure provides detailed information on hormonogenic and glycosylation sites. We employ liquid chromatography-mass spectrometry (LC-MS) to validate these findings as well as other post-translational modifications and proteolytic cleavage sites. Our results offer insights into thyroid hormonogenesis of native hTG and provide a fundamental understanding of clinically relevant mutations. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12073.map.gz | 9.6 MB | EMDB map data format | |
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Header (meta data) | emd-12073-v30.xml emd-12073.xml | 21.6 KB 21.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12073_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_12073.png | 227.1 KB | ||
Masks | emd_12073_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-12073.cif.gz | 7.8 KB | ||
Others | emd_12073_half_map_1.map.gz emd_12073_half_map_2.map.gz | 106.5 MB 106.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12073 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12073 | HTTPS FTP |
-Validation report
Summary document | emd_12073_validation.pdf.gz | 767.6 KB | Display | EMDB validaton report |
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Full document | emd_12073_full_validation.pdf.gz | 767.1 KB | Display | |
Data in XML | emd_12073_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | emd_12073_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12073 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12073 | HTTPS FTP |
-Related structure data
Related structure data | 7b75MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12073.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | human Thyroglobulin, composite map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.28 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12073_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_12073_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_12073_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : human thyroglobulin
Entire | Name: human thyroglobulin |
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Components |
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-Supramolecule #1: human thyroglobulin
Supramolecule | Name: human thyroglobulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: human thyroglobulin purified from thyroid gland tissue and non in vitro iodinated |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Thyroid / Tissue: Thyroid |
Molecular weight | Theoretical: 660 KDa |
-Macromolecule #1: Thyroglobulin
Macromolecule | Name: Thyroglobulin / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) / Organ: Thyroid / Tissue: Thyroid |
Molecular weight | Theoretical: 305.069844 KDa |
Sequence | String: MALVLEIFTL LASICWVSAN IFEYQVDAQP LRPCELQRET AFLKQADYVP QCAEDGSFQT VQCQNDGRSC WCVGANGSEV LGSRQPGRP VACLSFCQLQ KQQILLSGYI NSTDTSYLPQ CQDSGDYAPV QCDVQQVQCW CVDAEGMEVY GTRQLGRPKR C PRSCEIRN ...String: MALVLEIFTL LASICWVSAN IFEYQVDAQP LRPCELQRET AFLKQADYVP QCAEDGSFQT VQCQNDGRSC WCVGANGSEV LGSRQPGRP VACLSFCQLQ KQQILLSGYI NSTDTSYLPQ CQDSGDYAPV QCDVQQVQCW CVDAEGMEVY GTRQLGRPKR C PRSCEIRN RRLLHGVGDK SPPQCSAEGE FMPVQCKFVN TTDMMIFDLV HSYNRFPDAF VTFSSFQRRF PEVSGYCHCA DS QGRELAE TGLELLLDEI YDTIFAGLDL PSTFTETTLY RILQRRFLAV QSVISGRFRC PTKCEVERFT ATSFGHPYVP SCR RNGDYQ AVQCQTEGPC WCVDAQGKEM HGTRQQGEPP SCAEGQSCAS ERQQALSRLY FGTSGYFSQH DLFSSPEKRW ASPR VARFA TSCPPTIKEL FVDSGLLRPM VEGQSQQFSV SENLLKEAIR AIFPSRGLAR LALQFTTNPK RLQQNLFGGK FLVNV GQFN LSGALGTRGT FNFSQFFQQL GLASFLNGGR QEDLAKPLSV GLDSNSSTGT PEAAKKDGTM NKPTVGSFGF EINLQE NQN ALKFLASLLE LPEFLLFLQH AISVPEDVAR DLGDVMETVL SSQTCEQTPE RLFVPSCTTE GSYEDVQCFS GECWCVN SW GKELPGSRVR GGQPRCPTDC EKQRARMQSL MGSQPAGSTL FVPACTSEGH FLPVQCFNSE CYCVDAEGQA IPGTRSAI G KPKKCPTPCQ LQSEQAFLRT VQALLSNSSM LPTLSDTYIP QCSTDGQWRQ VQCNGPPEQV FELYQRWEAQ NKGQDLTPA KLLVKIMSYR EAASGNFSLF IQSLYEAGQQ DVFPVLSQYP SLQDVPLAAL EGKRPQPREN ILLEPYLFWQ ILNGQLSQYP GSYSDFSTP LAHFDLRNCW CVDEAGQELE GMRSEPSKLP TCPGSCEEAK LRVLQFIRET EEIVSASNSS RFPLGESFLV A KGIRLRNE DLGLPPLFPP REAFAEQFLR GSDYAIRLAA QSTLSFYQRR RFSPDDSAGA SALLRSGPYM PQCDAFGSWE PV QCHAGTG HCWCVDEKGG FIPGSLTARS LQIPQCPTTC EKSRTSGLLS SWKQARSQEN PSPKDLFVPA CLETGEYARL QAS GAGTWC VDPASGEELR PGSSSSAQCP SLCNVLKSGV LSRRVSPGYV PACRAEDGGF SPVQCDQAQG SCWCVMDSGE EVPG TRVTG GQPACESPRC PLPFNASEVV GGTILCETIS GPTGSAMQQC QLLCRQGSWS VFPPGPLICS LESGRWESQL PQPRA CQRP QLWQTIQTQG HFQLQLPPGK MCSADYADLL QTFQVFILDE LTARGFCQIQ VKTFGTLVSI PVCNNSSVQV GCLTRE RLG VNVTWKSRLE DIPVASLPDL HDIERALVGK DLLGRFTDLI QSGSFQLHLD SKTFPAETIR FLQGDHFGTS PRTWFGC SE GFYQVLTSEA SQDGLGCVKC PEGSYSQDEE CIPCPVGFYQ EQAGSLACVP CPVGRTTISA GAFSQTHCVT DCQRNEAG L QCDQNGQYRA SQKDRGSGKA FCVDGEGRRL PWWETEAPLE DSQCLMMQKF EKVPESKVIF DANAPVAVRS KVPDSEFPV MQCLTDCTED EACSFFTVST TEPEISCDFY AWTSDNVACM TSDQKRDALG NSKATSFGSL RCQVKVRSHG QDSPAVYLKK GQGSTTTLQ KRFEPTGFQN MLSGLYNPIV FSASGANLTD AHLFCLLACD RDLCCDGFVL TQVQGGAIIC GLLSSPSVLL C NVKDWMDP SEAWANATCP GVTYDQESHQ VILRLGDQEF IKSLTPLEGT QDTFTNFQQV YLWKDSDMGS RPESMGCRKD TV PRPASPT EAGLTTELFS PVDLNQVIVN GNQSLSSQKH WLFKHLFSAQ QANLWCLSRC VQEHSFCQLA EITESASLYF TCT LYPEAQ VCDDIMESNA QGCRLILPQM PKALFRKKVI LEDKVKNFYT RLPFQKLMGI SIRNKVPMSE KSISNGFFEC ERRC DADPC CTGFGFLNVS QLKGGEVTCL TLNSLGIQMC SEENGGAWRI LDCGSPDIEV HTYPFGWYQK PIAQNNAPSF CPLVV LPSL TEKVSLDSWQ SLALSSVVVD PSIRHFDVAH VSTAATSNFS AVRDLCLSEC SQHEACLITT LQTQPGAVRC MFYADT QSC THSLQGQNCR LLLREEATHI YRKPGISLLS YEASVPSVPI STHGRLLGRS QAIQVGTSWK QVDQFLGVPY AAPPLAE RR FQAPEPLNWT GSWDASKPRA SCWQPGTRTS TSPGVSEDCL YLNVFIPQNV APNASVLVFF HNTMDREESE GWPAIDGS F LAAVGNLIVV TASYRVGVFG FLSSGSGEVS GNWGLLDQVA ALTWVQTHIR GFGGDPRRVS LAADRGGADV ASIHLLTAR ATNSQLFRRA VLMGGSALSP AAVISHERAQ QQAIALAKEV SCPMSSSQEV VSCLRQKPAN VLNDAQTKLL AVSGPFHYWG PVIDGHFLR EPPARALKRS LWVEVDLLIG SSQDDGLINR AKAVKQFEES RGRTSSKTAF YQALQNSLGG EDSDARVEAA A TWYYSLEH STDDYASFSR ALENATRDYF IICPIIDMAS AWAKRARGNV FMYHAPENYG HGSLELLADV QFALGLPFYP AY EGQFSLE EKSLSLKIMQ YFSHFIRSGN PNYPYEFSRK VPTFATPWPD FVPRAGGENY KEFSELLPNR QGLKKADCSF WSK YISSLK TSADGAKGGQ SAESEEEELT AGSGLREDLL SLQEPGSKTY SK UniProtKB: Thyroglobulin |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 16 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
Details: 0.22 um filtered and degased | ||||||||||||
Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 293.15 K / Instrument: LEICA EM GP | ||||||||||||
Details | concentrated SEC peak |
-Electron microscopy
Microscope | TFS KRIOS |
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Temperature | Min: 80.0 K / Max: 80.0 K |
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Number real images: 8119 / Average exposure time: 10.0 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 78125 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 215000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7b75: |