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- EMDB-63489: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state... -

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Basic information

Entry
Database: EMDB / ID: EMD-63489
TitleA Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 1 conformation)
Map data
Sample
  • Complex: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 1 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 / G protein-coupled receptor internalization / arrestin family protein binding / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / osteoblast development ...parathyroid hormone receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / Activation of SMO / negative regulation of interleukin-8 production / G protein-coupled receptor internalization / arrestin family protein binding / Class B/2 (Secretin family receptors) / G protein-coupled peptide receptor activity / osteoblast development / Lysosome Vesicle Biogenesis / negative regulation of NF-kappaB transcription factor activity / positive regulation of inositol phosphate biosynthetic process / positive regulation of cardiac muscle hypertrophy / stress fiber assembly / Golgi Associated Vesicle Biogenesis / positive regulation of Rho protein signal transduction / bone mineralization / pseudopodium / peptide hormone binding / negative regulation of interleukin-6 production / positive regulation of receptor internalization / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / negative regulation of Notch signaling pathway / enzyme inhibitor activity / chondrocyte differentiation / bone resorption / cell maturation / insulin-like growth factor receptor binding / clathrin-coated pit / negative regulation of protein ubiquitination / GTPase activator activity / cytoplasmic vesicle membrane / Activated NOTCH1 Transmits Signal to the Nucleus / skeletal system development / G protein-coupled receptor binding / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / intracellular calcium ion homeostasis / 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 / Thrombin signalling through proteinase activated receptors (PARs) / Clathrin-mediated endocytosis / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / basolateral plasma membrane / molecular adaptor activity / in utero embryonic development / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / cell surface receptor signaling pathway / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / receptor complex / Ub-specific processing proteases / protein ubiquitination / nuclear body / apical plasma membrane / G protein-coupled receptor signaling pathway / Golgi membrane / negative regulation of cell population proliferation / lysosomal membrane / positive regulation of cell population proliferation / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / chromatin / nucleolus / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
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: 3.07 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-B-arrestin1 complex (state 1 conformation)
Authors: Zhao L / Yuan Q
History
DepositionFeb 19, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63489.png

Downloads & links

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Map

FileDownload / File: emd_63489.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: 0.338
Minimum - Maximum-1.0361298 - 3.00193
Average (Standard dev.)0.0071179997 (±0.038269516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1-1-1
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 1 conformation)
Components
  • Complex: A Cryo-EM structure of LA-PTH-PTH1R-Beta-arrestin1 complex (state 1 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 1 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: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107599
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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