[English] 日本語
Yorodumi
- EMDB-60404: Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60404
TitleCryo-EM structure focused on the receptor of the ET-1 bound ETBR-DNGI complex
Map datafull map
Sample
  • Complex: ET-1 BOUND ETBR COMPLEX
    • Protein or peptide: Endothelin receptor type B
    • Protein or peptide: Endothelin-1
KeywordsENDOTHELIN / RECEPTOR / Gi / COMPLEX / MEMBRANE PROTEIN
Function / homology
Function and homology information


enteric smooth muscle cell differentiation / response to endothelin / : / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / endothelin receptor activity ...enteric smooth muscle cell differentiation / response to endothelin / : / negative regulation of neuron maturation / endothelin A receptor binding / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / negative regulation of phospholipase C/protein kinase C signal transduction / endothelin receptor activity / peptide hormone secretion / endothelin B receptor binding / aldosterone metabolic process / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of artery morphogenesis / cellular response to mineralocorticoid stimulus / histamine secretion / neural crest cell fate commitment / regulation of fever generation / vein smooth muscle contraction / glomerular endothelium development / response to prostaglandin F / positive regulation of penile erection / sympathetic neuron axon guidance / positive regulation of sarcomere organization / noradrenergic neuron differentiation / leukocyte activation / body fluid secretion / maternal process involved in parturition / positive regulation of chemokine-mediated signaling pathway / rough endoplasmic reticulum lumen / heparin proteoglycan metabolic process / positive regulation of renal sodium excretion / neuroblast migration / : / posterior midgut development / pharyngeal arch artery morphogenesis / regulation of D-glucose transmembrane transport / positive regulation of odontogenesis / endothelin receptor signaling pathway involved in heart process / epithelial fluid transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / Weibel-Palade body / endothelin receptor signaling pathway / response to ozone / podocyte differentiation / developmental pigmentation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / response to sodium phosphate / renal sodium excretion / enteric nervous system development / positive regulation of cation channel activity / axonogenesis involved in innervation / glomerular filtration / protein transmembrane transport / renin secretion into blood stream / artery smooth muscle contraction / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / renal albumin absorption / melanocyte differentiation / positive regulation of prostaglandin secretion / respiratory gaseous exchange by respiratory system / regulation of pH / positive regulation of smooth muscle contraction / basal part of cell / peripheral nervous system development / response to salt / positive regulation of hormone secretion / type 1 angiotensin receptor binding / cellular response to toxic substance / negative regulation of adenylate cyclase activity / positive regulation of urine volume / regulation of systemic arterial blood pressure by endothelin / regulation of epithelial cell proliferation / vasoconstriction / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / establishment of endothelial barrier / signal transduction involved in regulation of gene expression / positive regulation of neutrophil chemotaxis / neural crest cell migration / prostaglandin biosynthetic process / superoxide anion generation / cellular response to glucocorticoid stimulus / cartilage development / middle ear morphogenesis / negative regulation of protein metabolic process / cGMP-mediated signaling / cellular response to fatty acid / nitric oxide transport / response to pain / branching involved in blood vessel morphogenesis / positive regulation of cardiac muscle hypertrophy
Similarity search - Function
Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / Serpentine type 7TM GPCR chemoreceptor Srsx ...Endothelin receptor B / Endothelin receptor family / Endothelin-like toxin / Endothelin-like toxin, conserved site / Endothelin / : / Endothelin family / Endothelin family signature. / Endothelin / Serpentine type 7TM GPCR chemoreceptor Srsx / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Endothelin-1 / Endothelin receptor type B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.62 Å
AuthorsTani K / Maki-Yonekura S / Kanno R / Negami T / Hamaguchi T / Hall M / Mizoguchi A / Humbel BM / Terada T / Yonekura K / Doi T
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121004 Japan
Japan Society for the Promotion of Science (JSPS)20H03210 Japan
CitationJournal: Commun Biol / Year: 2024
Title: Structure of endothelin ET receptor-G complex in a conformation stabilized by unique NPxxL motif.
Authors: Kazutoshi Tani / Saori Maki-Yonekura / Ryo Kanno / Tatsuki Negami / Tasuku Hamaguchi / Malgorzata Hall / Akira Mizoguchi / Bruno M Humbel / Tohru Terada / Koji Yonekura / Tomoko Doi /
Abstract: Endothelin type B receptor (ETR) plays a crucial role in regulating blood pressure and humoral homeostasis, making it an important therapeutic target for related diseases. ETR activation by the ...Endothelin type B receptor (ETR) plays a crucial role in regulating blood pressure and humoral homeostasis, making it an important therapeutic target for related diseases. ETR activation by the endogenous peptide hormones endothelin (ET)-1-3 stimulates several signaling pathways, including G, G, G, G, and β-arrestin. Although the conserved NPxxY motif in transmembrane helix 7 (TM7) is important during GPCR activation, ETR possesses the lesser known NPxxL motif. In this study, we present the cryo-EM structure of the ETR-G complex, complemented by MD simulations and functional studies. These investigations reveal an unusual movement of TM7 to the intracellular side during ETR activation and the essential roles of the diverse NPxxL motif in stabilizing the active conformation of ETR and organizing the assembly of the binding pocket for the α5 helix of G protein. These findings enhance our understanding of the interactions between GPCRs and G proteins, thereby advancing the development of therapeutic strategies.
History
DepositionJun 5, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_60404.png

Downloads & links

-
Map

FileDownload / File: emd_60404.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 192 pix.
= 228.48 Å		1.19 Å/pix.
x 192 pix.
= 228.48 Å		1.19 Å/pix.
x 192 pix.
= 228.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.16544221 - 0.21601684
Average (Standard dev.)-0.00010962154 (±0.0041943165)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 228.48001 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half-odd map

Fileemd_60404_half_map_1.map
Annotationhalf-odd map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half-even map

Fileemd_60404_half_map_2.map
Annotationhalf-even map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ET-1 BOUND ETBR COMPLEX

EntireName: ET-1 BOUND ETBR COMPLEX
Components
  • Complex: ET-1 BOUND ETBR COMPLEX
    • Protein or peptide: Endothelin receptor type B
    • Protein or peptide: Endothelin-1

-
Supramolecule #1: ET-1 BOUND ETBR COMPLEX

SupramoleculeName: ET-1 BOUND ETBR COMPLEX / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Endothelin receptor type B

MacromoleculeName: Endothelin receptor type B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.808262 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: PGGGLAPAEV PKGDRTAGSP PRTISPPPCQ GPIEIKETFK YINTVVSCLV FVLGIIGNST LLYIIYKNKC MRNGPNILIA SLALGDLLH IVIDIPINVY KLLAEDWPFG AEMCKLVPFI QKASVGITVL SLCALSIDRY RAVASWSRIK GIGVPKWTAV E IVLIWVVS ...String:
PGGGLAPAEV PKGDRTAGSP PRTISPPPCQ GPIEIKETFK YINTVVSCLV FVLGIIGNST LLYIIYKNKC MRNGPNILIA SLALGDLLH IVIDIPINVY KLLAEDWPFG AEMCKLVPFI QKASVGITVL SLCALSIDRY RAVASWSRIK GIGVPKWTAV E IVLIWVVS VVLAVPEAIG FDIITMDYKG SYLRICLLHP VQKTAFMQFY KTAKDWWLFS FYFCLPLAIT AFFYTLMTCE ML RKKSGMQ IALNDHLKQR REVAKTVFCL VLVFALCWLP LHLSRILKLT LYNQNDPNRC ELLSFLLVLD YIGINMASLN SCI NPIALY LVSKRFKNAF KSALCCWAQS

UniProtKB: Endothelin receptor type B

-
Macromolecule #2: Endothelin-1

MacromoleculeName: Endothelin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.497951 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
CSCSSLMDKE CVYFCHLDII W

UniProtKB: Endothelin-1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE
DetailsThis sample was monodisperse.

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 401671
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-8zrt:
Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-DNGI complex

+
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