[English] 日本語
Yorodumi
- EMDB-63500: A Cryo-EM structure of LA-PTH-PTH1R-V2RT-Beta-arrestin1 complex (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-63500
TitleA Cryo-EM structure of LA-PTH-PTH1R-V2RT-Beta-arrestin1 complex (state 1 conformation)
Map data
Sample
  • Complex: A Cryo-EM structure of LA-PTH-PTH1R-V2R-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,Vasopressin V2 receptor
KeywordsPTH1R / arrestin / GPCR / MEMBRANE PROTEIN
Function / homology
Function and homology information


renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / parathyroid hormone receptor activity / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / hemostasis / Activation of SMO ...renal water retention / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / parathyroid hormone receptor activity / Vasopressin-like receptors / regulation of systemic arterial blood pressure by vasopressin / vasopressin receptor activity / angiotensin receptor binding / TGFBR3 regulates TGF-beta signaling / hemostasis / Activation of SMO / telencephalon development / negative regulation of interleukin-8 production / arrestin family protein binding / Class B/2 (Secretin family receptors) / G protein-coupled receptor internalization / G protein-coupled peptide receptor activity / osteoblast development / Lysosome Vesicle Biogenesis / : / stress fiber assembly / positive regulation of cardiac muscle hypertrophy / positive regulation of inositol phosphate biosynthetic process / Golgi Associated Vesicle Biogenesis / bone mineralization / positive regulation of Rho protein signal transduction / pseudopodium / positive regulation of systemic arterial blood pressure / negative regulation of interleukin-6 production / peptide hormone binding / positive regulation of intracellular signal transduction / positive regulation of receptor internalization / positive regulation of vasoconstriction / negative regulation of Notch signaling pathway / endocytic vesicle / chondrocyte differentiation / bone resorption / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / activation of adenylate cyclase activity / cellular response to hormone stimulus / insulin-like growth factor receptor binding / cell maturation / response to cytokine / clathrin-coated pit / negative regulation of protein ubiquitination / enzyme inhibitor activity / GTPase activator activity / Activated NOTCH1 Transmits Signal to the Nucleus / cytoplasmic vesicle membrane / skeletal system development / clathrin-coated endocytic vesicle membrane / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / G protein-coupled receptor binding / G protein-coupled receptor activity / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of protein phosphorylation / 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 / Vasopressin regulates renal water homeostasis via Aquaporins / Cargo recognition for clathrin-mediated endocytosis / protein transport / Clathrin-mediated endocytosis / Thrombin signalling through proteinase activated receptors (PARs) / cytoplasmic vesicle / basolateral plasma membrane / G alpha (s) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / ubiquitin-dependent protein catabolic process / in utero embryonic development / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / receptor complex / cell population proliferation / apical plasma membrane / endosome / Ub-specific processing proteases / nuclear body / protein ubiquitination / 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 / positive regulation of gene expression / regulation of transcription by RNA polymerase II / chromatin / nucleolus / perinuclear region of cytoplasm / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Vasopressin V2 receptor / GPCR, family 2, parathyroid hormone receptor / Vasopressin 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 ...Vasopressin V2 receptor / GPCR, family 2, parathyroid hormone receptor / Vasopressin 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. / G-protein coupled receptors family 1 signature. / 7 transmembrane receptor (rhodopsin family) / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / Immunoglobulin E-set
Similarity search - Domain/homology
Vasopressin V2 receptor / Beta-arrestin-1 / Parathyroid hormone/parathyroid hormone-related peptide receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_63500.png

Downloads & links

-
Map

FileDownload / File: emd_63500.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: 0.31
Minimum - Maximum-1.7250617 - 3.0066175
Average (Standard dev.)0.00662805 (±0.03660032)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
Entire : A Cryo-EM structure of LA-PTH-PTH1R-V2R-Beta-arrestin1 complex (s...

EntireName: A Cryo-EM structure of LA-PTH-PTH1R-V2R-Beta-arrestin1 complex (state 1 conformation)
Components
  • Complex: A Cryo-EM structure of LA-PTH-PTH1R-V2R-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,Vasopressin V2 receptor

-
Supramolecule #1: A Cryo-EM structure of LA-PTH-PTH1R-V2R-Beta-arrestin1 complex (s...

SupramoleculeName: A Cryo-EM structure of LA-PTH-PTH1R-V2R-Beta-arrestin1 complex (state 1 conformation)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
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: 43.995246 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 ETPVDTNLIE LDTNDDDAAA EDFAR

UniProtKB: Beta-arrestin-1

-
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: 25.551494 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 KTHHHHHHH

-
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: 23.244842 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYKYVPVTFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QYKYVPVTFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGE

-
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

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

MacromoleculeName: Parathyroid hormone/parathyroid hormone-related peptide receptor,Vasopressin V2 receptor
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.901793 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 SSYSYGPMVS HARGR TPPS LGPQDESC(TPO)(TPO) A(SEP)(SEP)(SEP)LAKDTS SGS

UniProtKB: Parathyroid hormone/parathyroid hormone-related peptide receptor, Vasopressin V2 receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.04
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80488
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more