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- EMDB-44504: Cryo-EM structure of Bride of Sevenless extracellular domain (dim... -

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Basic information

Entry
Database: EMDB / ID: EMD-44504
TitleCryo-EM structure of Bride of Sevenless extracellular domain (dimer, Sevenless-bound form)
Map dataSharpened map
Sample
  • Organelle or cellular component: Bride of Sevenless extracellular domain
    • Protein or peptide: Protein bride of sevenless
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsbride of sevenless / boss / GPCR / G-protein coupled receptor / drosophila / eye development / vision / photoreceptor / glucose metabolism / SIGNALING PROTEIN
Function / homology
Function and homology information


R8 cell-mediated photoreceptor organization / rhabdomere microvillus membrane / sevenless binding / germ-line stem-cell niche homeostasis / R7 cell fate commitment / sevenless signaling pathway / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / lipid homeostasis / response to glucose / visual perception ...R8 cell-mediated photoreceptor organization / rhabdomere microvillus membrane / sevenless binding / germ-line stem-cell niche homeostasis / R7 cell fate commitment / sevenless signaling pathway / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / lipid homeostasis / response to glucose / visual perception / glucose homeostasis / receptor ligand activity / plasma membrane
Similarity search - Function
Bride of sevenless protein / : / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
Protein bride of sevenless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsCerutti G / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mol Cell / Year: 2024
Title: Structures and pH-dependent dimerization of the sevenless receptor tyrosine kinase.
Authors: Gabriele Cerutti / Ronald Arias / Fabiana Bahna / Seetha Mannepalli / Phinikoula S Katsamba / Goran Ahlsen / Brian Kloss / Renato Bruni / Andrew Tomlinson / Lawrence Shapiro /
Abstract: Sevenless (Sev) is a Drosophila receptor tyrosine kinase (RTK) required for the specification of the R7 photoreceptor. It is cleaved into α and β subunits and binds the ectodomain of the G-protein- ...Sevenless (Sev) is a Drosophila receptor tyrosine kinase (RTK) required for the specification of the R7 photoreceptor. It is cleaved into α and β subunits and binds the ectodomain of the G-protein-coupled receptor bride of sevenless (Boss). Previous work showed that the Boss ectodomain could bind but not activate Sev; rather, the whole seven-pass transmembrane Boss was required. Here, we show that Sev does not need to be cleaved to function and that a single-pass transmembrane form of Boss activates Sev. We use cryo-electron microscopy and biophysical methods to determine the structural basis of ligand binding and pH-dependent dimerization of Sev, and we discuss the implications in the process of Sev activation. The Sev human homolog, receptor oncogene from sarcoma 1 (ROS1), is associated with oncogenic transformations, and we discuss their structural similarities.
History
DepositionApr 18, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44504.png

Downloads & links

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Map

FileDownload / File: emd_44504.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.1805067 - 2.0801432
Average (Standard dev.)0.00007570057 (±0.033102408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_44504_additional_1.map
AnnotationUnsharpened map
Projections & Slices
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Additional map: Density-modified map (deepEMhancer)

Fileemd_44504_additional_2.map
AnnotationDensity-modified map (deepEMhancer)
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Additional map: C1 map resampled on the grid of the main map

Fileemd_44504_additional_3.map
AnnotationC1 map resampled on the grid of the main map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_44504_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_44504_half_map_2.map
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Sample components

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Entire : Bride of Sevenless extracellular domain

EntireName: Bride of Sevenless extracellular domain
Components
  • Organelle or cellular component: Bride of Sevenless extracellular domain
    • Protein or peptide: Protein bride of sevenless
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Bride of Sevenless extracellular domain

SupramoleculeName: Bride of Sevenless extracellular domain / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Protein bride of sevenless

MacromoleculeName: Protein bride of sevenless / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 57.278723 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CHGADLTSPT KKSAPLRITK PQPTSQQAKP ISITTRAPTT VASTTDDEVS SSVDGQLAPL ISSTTEGPSS GTTASLVPEI CLNGLQLTV NSADEGTVIR KQEEFVKILE GDVVLSVLTK DPDSALFVIN RVNQANLIMA DFEIGIRAIS IDNASLAENL L IQEVQFLQ ...String:
CHGADLTSPT KKSAPLRITK PQPTSQQAKP ISITTRAPTT VASTTDDEVS SSVDGQLAPL ISSTTEGPSS GTTASLVPEI CLNGLQLTV NSADEGTVIR KQEEFVKILE GDVVLSVLTK DPDSALFVIN RVNQANLIMA DFEIGIRAIS IDNASLAENL L IQEVQFLQ QCTTYSMGIF VDWELYKQLE SVIKDLEYNI WPIPGTRAHL FPKVAHLLHQ MPWGEKIASV EIATETLEMY NE FMEAARQ EHMCLMHFKS DDNVYIMFGN KLASHFKENG TLFSVPTDRT DDEFLADLPN RAFVLMENEI DLSTAVELDA TPT ALDEIL IGKSVLPSRV LSFAGSIIDL MNWLRGSLSK HCKRGEEHDL YVLESCFNFL NFIEDWRTSE YRQAHDTAEI LSLL LMRKL GTAMNFQMYQ KKVLTLDKIT GESRTELREI ASQNFVTNVT TYYHYNRDNH TSLELKTKFG QVFNCQYSAG DNRRY PFLF DGESVMFWRI KMDTWHHHHH H

UniProtKB: Protein bride of sevenless

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Macromolecule #2: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: 6.6
GridMaterial: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 51.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 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: PDB ENTRY
PDB model - PDB ID:

9bfq

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 187282
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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