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- EMDB-60404: Cryo-EM structure focused on the receptor of the ET-1 bound ETBR-... -

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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 / aldosterone metabolic process / positive regulation of prostaglandin-endoperoxide synthase activity / negative regulation of neuron maturation / endothelin A receptor binding / protein kinase C deactivation / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation ...enteric smooth muscle cell differentiation / response to endothelin / aldosterone metabolic process / positive regulation of prostaglandin-endoperoxide synthase activity / negative regulation of neuron maturation / endothelin A receptor binding / protein kinase C deactivation / chordate pharynx development / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / endothelin receptor activity / peptide hormone secretion / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / positive regulation of artery morphogenesis / body fluid secretion / neural crest cell fate commitment / vein smooth muscle contraction / regulation of fever generation / sympathetic neuron axon guidance / response to prostaglandin F / glomerular endothelium development / positive regulation of sarcomere organization / noradrenergic neuron differentiation / semaphorin-plexin signaling pathway involved in axon guidance / histamine secretion / positive regulation of renal sodium excretion / leukocyte activation / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / positive regulation of penile erection / neuroblast migration / heparin metabolic process / rough endoplasmic reticulum lumen / pharyngeal arch artery morphogenesis / posterior midgut development / regulation of D-glucose transmembrane transport / positive regulation of odontogenesis / epithelial fluid transport / response to leptin / endothelin receptor signaling pathway involved in heart process / negative regulation of hormone secretion / cardiac neural crest cell migration involved in outflow tract morphogenesis / Weibel-Palade body / endothelin receptor signaling pathway / response to ozone / developmental pigmentation / podocyte differentiation / positive regulation of cell growth involved in cardiac muscle cell development / renal sodium ion absorption / artery smooth muscle contraction / response to sodium phosphate / glomerular filtration / melanocyte differentiation / protein transmembrane transport / renal sodium excretion / enteric nervous system development / axonogenesis involved in innervation / positive regulation of cation channel activity / renin secretion into blood stream / cellular response to follicle-stimulating hormone stimulus / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / negative regulation of nitric-oxide synthase biosynthetic process / cellular response to mineralocorticoid stimulus / renal albumin absorption / basal part of cell / positive regulation of smooth muscle contraction / respiratory gaseous exchange by respiratory system / peripheral nervous system development / regulation of pH / response to salt / positive regulation of urine volume / positive regulation of hormone secretion / negative regulation of adenylate cyclase activity / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / : / regulation of epithelial cell proliferation / negative regulation of blood coagulation / type 1 angiotensin receptor binding / embryonic heart tube development / dorsal/ventral pattern formation / axon extension / superoxide anion generation / establishment of endothelial barrier / positive regulation of neutrophil chemotaxis / positive regulation of signaling receptor activity / cartilage development / middle ear morphogenesis / : / neural crest cell migration / cellular response to glucocorticoid stimulus / negative regulation of protein metabolic process / prostaglandin biosynthetic process / cellular response to fatty acid / nitric oxide transport / positive regulation of heart rate / branching involved in blood vessel morphogenesis
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 ETB receptor-Gi complex in a conformation stabilized by the unique NPxxL motif
Authors: Tani K / Maki-Yonekura S / Kanno R / Negami T / Hamaguchi T / Hall M / Mizoguchi A / Humbel BM / Terada T / Yonekura K / Doi T
History
DepositionJun 5, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60404.png

Downloads & links

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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 °

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Supplemental data

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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)

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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)

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Sample components

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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

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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)

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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

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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

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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

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

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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

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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)

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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

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