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- EMDB-61746: Cryo-EM structure of PTH-PTH1R-Gq (upright state) -

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Basic information

Entry
Database: EMDB / ID: EMD-61746
TitleCryo-EM structure of PTH-PTH1R-Gq (upright state)
Map datacomposite map (sharpened)
Sample
  • Complex: PTH-PTH1R-Gq complex
    • Complex: mini-G
      • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha-1 (miniGq)
    • Complex: Gprotein beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Gprotein gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: scFv16
      • Protein or peptide: scFv16
    • Complex: parathyroid hormone
      • Protein or peptide: Parathyroid hormone
    • Complex: parathyroid hormone 1 receptor
      • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Ligand: water
KeywordsClass B GPCRs / Gq / PTH / SIGNALING PROTEIN / SIGNALING PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / macromolecule biosynthetic process / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / parathyroid hormone receptor activity / hormone-mediated apoptotic signaling pathway ...parathyroid hormone receptor binding / type 1 parathyroid hormone receptor binding / negative regulation of bone mineralization involved in bone maturation / macromolecule biosynthetic process / positive regulation of osteoclast proliferation / negative regulation of apoptotic process in bone marrow cell / response to parathyroid hormone / positive regulation of cell proliferation in bone marrow / parathyroid hormone receptor activity / hormone-mediated apoptotic signaling pathway / magnesium ion homeostasis / positive regulation of signal transduction / response to fibroblast growth factor / phosphate ion homeostasis / cAMP metabolic process / G-protein activation / Activation of the phototransduction cascade / Glucagon-type ligand receptors / Thromboxane signalling through TP receptor / Sensory perception of sweet, bitter, and umami (glutamate) taste / G beta:gamma signalling through PI3Kgamma / G beta:gamma signalling through CDC42 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Ca2+ pathway / G alpha (z) signalling events / response to vitamin D / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / Vasopressin regulates renal water homeostasis via Aquaporins / Adrenaline,noradrenaline inhibits insulin secretion / negative regulation of chondrocyte differentiation / ADP signalling through P2Y purinoceptor 12 / G alpha (q) signalling events / osteoblast development / G alpha (i) signalling events / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (12/13) signalling events / Glucagon-type ligand receptors / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Adrenaline,noradrenaline inhibits insulin secretion / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Ca2+ pathway / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / photoreceptor outer segment membrane / G alpha (q) signalling events / positive regulation of inositol phosphate biosynthetic process / G alpha (i) signalling events / spectrin binding / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / peptide hormone receptor binding / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / Vasopressin regulates renal water homeostasis via Aquaporins / bone mineralization / alkylglycerophosphoethanolamine phosphodiesterase activity / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / photoreceptor outer segment / Rho protein signal transduction / chondrocyte differentiation / positive regulation of glycogen biosynthetic process / bone resorption / positive regulation of bone mineralization / response to cadmium ion / cell maturation / photoreceptor inner segment / cardiac muscle cell apoptotic process / homeostasis of number of cells within a tissue / skeletal system development / positive regulation of D-glucose import / response to lead ion / hormone activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cellular response to catecholamine stimulus / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / cell-cell signaling / sensory perception of taste / signaling receptor complex adaptor activity
Similarity search - Function
Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. ...Parathyroid hormone / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / GPCR, family 2, parathyroid hormone receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Parathyroid hormone / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human) / Rattus rattus (black rat) / Bos taurus (domestic cattle) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsSano FK / Hirano H / Itoh Y / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Chem Biol / Year: 2025
Title: Insights into G-protein coupling preference from cryo-EM structures of G-bound PTH1R.
Authors: Fumiya K Sano / Kota Shimizume / Kazuhiro Kobayashi / Toshikuni Awazu / Kouki Kawakami / Hiroaki Akasaka / Takaaki A Kobayashi / Tatsuki Tanaka / Hiroyuki H Okamoto / Hisato Hirano / Tsukasa ...Authors: Fumiya K Sano / Kota Shimizume / Kazuhiro Kobayashi / Toshikuni Awazu / Kouki Kawakami / Hiroaki Akasaka / Takaaki A Kobayashi / Tatsuki Tanaka / Hiroyuki H Okamoto / Hisato Hirano / Tsukasa Kusakizako / Wataru Shihoya / Yoshiaki Kise / Yuzuru Itoh / Ryuichiro Ishitani / Yasushi Okada / Yasushi Sako / Masataka Yanagawa / Asuka Inoue / Osamu Nureki /
Abstract: The parathyroid hormone type 1 receptor (PTH1R) is a prototypical class B1 G-protein-coupled receptor that couples to both G and G, having a crucial role in calcium homeostasis and serving as a ...The parathyroid hormone type 1 receptor (PTH1R) is a prototypical class B1 G-protein-coupled receptor that couples to both G and G, having a crucial role in calcium homeostasis and serving as a therapeutic target for osteoporosis. Therapies targeting PTH1R face challenges because of G-associated prolonged signaling, which leads to bone resorption. To address this, selective activation of G signaling is desirable. However, the structural basis of G-mediated signaling remains unclear, limiting the development of signal-selective drugs. Here, we present cryo-electron microscopy structures of the PTH1R-G complex in two distinct extracellular conformations, demonstrating the role of N-linked glycans at N176 in stabilizing the ligand-tilted conformation. Comparison with a G-bound PTH1R structure highlights the role of key interactions involving both the C terminus of Gα and the receptor's intracellular loop 2 in G signaling. These structural insights provide a foundation for understanding the molecular mechanisms of PTH1R signaling.
History
DepositionSep 29, 2024-
Header (metadata) releaseOct 16, 2024-
Map releaseOct 16, 2024-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61746.png

Downloads & links

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Map

FileDownload / File: emd_61746.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map (sharpened)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.49 Å/pix.
x 380 pix.
= 186.96 Å		0.49 Å/pix.
x 380 pix.
= 186.96 Å		0.49 Å/pix.
x 380 pix.
= 186.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.492 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.97
Minimum - Maximum-40.844543000000002 - 54.093864000000004
Average (Standard dev.)0.0010527933 (±1.6500605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin808080
Dimensions380380380
Spacing380380380
CellA=B=C: 186.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: composite map (unsharpened)

Fileemd_61746_additional_1.map
Annotationcomposite map (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PTH-PTH1R-Gq complex

EntireName: PTH-PTH1R-Gq complex
Components
  • Complex: PTH-PTH1R-Gq complex
    • Complex: mini-G
      • Protein or peptide: Guanine nucleotide-binding protein G(q) subunit alpha-1 (miniGq)
    • Complex: Gprotein beta-1
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
    • Complex: Gprotein gamma-2
      • Protein or peptide: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
    • Complex: scFv16
      • Protein or peptide: scFv16
    • Complex: parathyroid hormone
      • Protein or peptide: Parathyroid hormone
    • Complex: parathyroid hormone 1 receptor
      • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor
  • Ligand: water

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Supramolecule #1: PTH-PTH1R-Gq complex

SupramoleculeName: PTH-PTH1R-Gq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: mini-G

SupramoleculeName: mini-G / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Gprotein beta-1

SupramoleculeName: Gprotein beta-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Rattus rattus (black rat)

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Supramolecule #4: Gprotein gamma-2

SupramoleculeName: Gprotein gamma-2 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #5: scFv16

SupramoleculeName: scFv16 / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #6: parathyroid hormone

SupramoleculeName: parathyroid hormone / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human) / Synthetically produced: Yes

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Supramolecule #7: parathyroid hormone 1 receptor

SupramoleculeName: parathyroid hormone 1 receptor / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanine nucleotide-binding protein G(q) subunit alpha-1 (miniGq)

MacromoleculeName: Guanine nucleotide-binding protein G(q) subunit alpha-1 (miniGq)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.953635 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSTVSAEDKA AAERSKMIDK NLREDGEKAR RTLRLLLLGA DNSGKSTIVK QMRILHGGSG GSGGTSGIFE TKFQVDKVNF HMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNDFKSIWN NRWLRTISVI LFLNKQDLLA EKVLAGKSKI E DYFPEFAR ...String:
GSTVSAEDKA AAERSKMIDK NLREDGEKAR RTLRLLLLGA DNSGKSTIVK QMRILHGGSG GSGGTSGIFE TKFQVDKVNF HMFDVGGQR DERRKWIQCF NDVTAIIFVV DSSDYNRLQE ALNDFKSIWN NRWLRTISVI LFLNKQDLLA EKVLAGKSKI E DYFPEFAR YTTPEDATPE PGEDPRVTRA KYFIRKEFVD ISTASGDGRH ICYPHFTCAV DTENARRIFN DCKDIILQMN LR EYNLV

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Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus rattus (black rat)
Molecular weightTheoretical: 37.79927 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSQLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String:
GSQLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWN

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1

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Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

MacromoleculeName: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 7.416489 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
ASNNTASIAQ ARKLVEQLKM EANIDRIKVS KAAADLMAYC EAHAKEDPLL TPVPASENPF REKKFFS

UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2

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Macromolecule #4: scFv16

MacromoleculeName: scFv16 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.720795 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String:
DVQLVESGGG LVQPGGSRKL SCSASGFAFS SFGMHWVRQA PEKGLEWVAY ISSGSGTIYY ADTVKGRFTI SRDDPKNTLF LQMTSLRSE DTAMYYCVRS IYYYGSSPFD FWGQGTTLTV SSGGGGSGGG GSGGGGSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL KAAAASSEDL YFQ

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Macromolecule #5: Parathyroid hormone

MacromoleculeName: Parathyroid hormone / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.123786 KDa
SequenceString:
SVSEIQLMHN LGKHLNSMER VEWLRKKLQD VHNF(NH2)

UniProtKB: Parathyroid hormone

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Macromolecule #6: Parathyroid hormone/parathyroid hormone-related peptide receptor

MacromoleculeName: Parathyroid hormone/parathyroid hormone-related peptide receptor
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.846227 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASGK LYPESEEDKE APTGSRYRGR PCLPEWDHI LCWPLGAPGE VVAVPCPDYI YDFNHKGHAY RRCDRNGSWE LVPGHNRTWA NYSECVKFLT NETREREVFD R LGMIYTVG ...String:
DADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASGK LYPESEEDKE APTGSRYRGR PCLPEWDHI LCWPLGAPGE VVAVPCPDYI YDFNHKGHAY RRCDRNGSWE LVPGHNRTWA NYSECVKFLT NETREREVFD R LGMIYTVG YSVSLASLTV AVLILAYFRR LHCTRNYIHM HLFLSFMLRA VSIFVKDAVL YSGATLDEAE RLTEEELRAI AQ APPPPAT AAAGYAGCRV AVTFFLYFLA TNYYWILVEG LYLHSLIFMA FFSEKKYLWG FTVFGWGLPA VFVAVWVSVR ATL ANTGCW DLSSGNKKWI IQVPILASIV LNFILFINIV RVLATKLRET NAGRCDTRQQ YRKLLKSTLV LMPLFGVHYI VFMA TPYTE VSGTLWQVQM HYEMLFNSFQ GFFVAIIYCF CNGEVQAEIK KSWSRWTLAL DFKRKARSGS SSYSYGPMVS HTSVT NVGP RVGLGLPLSP RLLPTATTNG HPQLPGHAKP GTPALETLET TPPAMAAPKD DGFLNGSCSG LDEEASGPER PPALLQ EEW ETVM

UniProtKB: Parathyroid hormone/parathyroid hormone-related peptide receptor

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1 / 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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 265775
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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