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- EMDB-63488: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state... -

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Basic information

Entry
Database: EMDB / ID: EMD-63488
TitleA Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 2 conformation)
Map data
Sample
  • Complex: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 2 conformation)
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30H
    • Protein or peptide: Fab30L
    • Protein or peptide: LA-PTH
    • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor
KeywordsPTH1R / arrestin / GPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


parathyroid hormone receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / desensitization of G protein-coupled receptor signaling pathway / bone resorption / osteoblast development / arrestin family protein binding / Class B/2 (Secretin family receptors) ...parathyroid hormone receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / desensitization of G protein-coupled receptor signaling pathway / bone resorption / osteoblast development / arrestin family protein binding / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / G protein-coupled receptor internalization / sensory perception / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / negative regulation of interleukin-6 production / Lysosome Vesicle Biogenesis / bone mineralization / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / chondrocyte differentiation / positive regulation of inositol phosphate biosynthetic process / pseudopodium / peptide hormone binding / negative regulation of Notch signaling pathway / positive regulation of receptor internalization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / cell maturation / insulin-like growth factor receptor binding / skeletal system development / negative regulation of protein ubiquitination / clathrin-coated pit / intracellular glucose homeostasis / cytoplasmic vesicle membrane / negative regulation of canonical NF-kappaB signal transduction / enzyme inhibitor activity / Activated NOTCH1 Transmits Signal to the Nucleus / GTPase activator activity / in utero embryonic development / cell population proliferation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / positive regulation of protein phosphorylation / intracellular calcium ion homeostasis / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / endocytic vesicle membrane / Signaling by BRAF and RAF1 fusions / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic vesicle / molecular adaptor activity / G alpha (s) signalling events / ubiquitin-dependent protein catabolic process / basolateral plasma membrane / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of ERK1 and ERK2 cascade / transcription coactivator activity / signaling receptor complex / cell surface receptor signaling pathway / apical plasma membrane / Ub-specific processing proteases / protein ubiquitination / G protein-coupled receptor signaling pathway / negative regulation of cell population proliferation / Golgi membrane / lysosomal membrane / positive regulation of cell population proliferation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / nucleolus / chromatin / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA-templated transcription / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GPCR, family 2, parathyroid hormone receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain ...GPCR, family 2, parathyroid hormone receptor / Arrestin, conserved site / Arrestins signature. / Arrestin / Arrestin, N-terminal / Arrestin-like, N-terminal / Arrestin C-terminal-like domain / Arrestin (or S-antigen), N-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin (or S-antigen), C-terminal domain / Arrestin-like, C-terminal / 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. / Immunoglobulin E-set
Similarity search - Domain/homology
Beta-arrestin-1 / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhao L / Yuan Q
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 2 conformation)
Authors: Zhao L / Yuan Q
History
DepositionFeb 19, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63488.png

Downloads & links

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Map

FileDownload / File: emd_63488.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å		0.73 Å/pix.
x 440 pix.
= 321.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.273
Minimum - Maximum-1.4808983 - 3.698718
Average (Standard dev.)0.006266422 (±0.034003913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 321.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state...

EntireName: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 2 conformation)
Components
  • Complex: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 2 conformation)
    • Protein or peptide: Beta-arrestin-1
    • Protein or peptide: Fab30H
    • Protein or peptide: Fab30L
    • Protein or peptide: LA-PTH
    • Protein or peptide: Parathyroid hormone/parathyroid hormone-related peptide receptor

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Supramolecule #1: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state...

SupramoleculeName: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 2 conformation)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Beta-arrestin-1

MacromoleculeName: Beta-arrestin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.131391 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKGTRVFKKA SCNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTCAFR YGREDLDVLG LTFRKDLFCA NVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPCSVTLQP GPEDTGKACG VDYEVKAFCA ENLEEKIHKR N SVRLVIRK ...String:
MKGTRVFKKA SCNGKLTVYL GKRDFVDHID LVDPVDGVVL VDPEYLKERR VYVTLTCAFR YGREDLDVLG LTFRKDLFCA NVQSFPPAP EDKKPLTRLQ ERLIKKLGEH AYPFTFEIPP NLPCSVTLQP GPEDTGKACG VDYEVKAFCA ENLEEKIHKR N SVRLVIRK VQYAPERPGP QPTAETTRQF LMSDKPLHLE ASLDKEIYYH GEPISVNVHV TNNTNKTVKK IKISVRQYAD IC LFNTAQY KCPVAMEEAD DTVAPSSTFC KVYTLTPFLC NNREKRGLAL DGKLKHEDTN LASSTLLREG ANREILGIIV SYK VKVKLV VSRGGLLGDL ASSDVAVELP FTLMHPKPKE EPPHREVPEN ETPVDTNL

UniProtKB: Beta-arrestin-1

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Macromolecule #2: Fab30H

MacromoleculeName: Fab30H / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.584467 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNVYSSSIHW VRQAPGKGLE WVASISSYYC YTYYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARSRQFWYS GLDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
MEISEVQLVE SGGGLVQPGG SLRLSCAASG FNVYSSSIHW VRQAPGKGLE WVASISSYYC YTYYADSVKG RFTISADTSK NTAYLQMNS LRAEDTAVYY CARSRQFWYS GLDYWGQGTL VTVSSASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKSCD KT

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Macromolecule #3: Fab30L

MacromoleculeName: Fab30L / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.435064 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQYKYVPVTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #4: LA-PTH

MacromoleculeName: LA-PTH / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.274027 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
AVAEIQLMHQ RAKWIQDARR RAFLHKLIAE IHTAEI

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Macromolecule #5: Parathyroid hormone/parathyroid hormone-related peptide receptor

MacromoleculeName: Parathyroid hormone/parathyroid hormone-related peptide receptor
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.344168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 SSYSYGPMV(SEP) H (TPO)(SEP)V(TPO)NG

UniProtKB: Parathyroid hormone/parathyroid hormone-related peptide receptor

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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: 7.04
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 18.0 µm / Nominal defocus min: 8.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101089
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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