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- EMDB-44503: Cryo-EM structure of Sevenless in complex with Bride of Sevenless -

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Basic information

Entry
Database: EMDB / ID: EMD-44503
TitleCryo-EM structure of Sevenless in complex with Bride of Sevenless
Map dataSharpened map
Sample
  • Complex: Sevenless extracellular domain in complex with Bride of Sevenless extracellular domain
    • Protein or peptide: Protein sevenless
    • Protein or peptide: Protein bride of sevenless
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordssevenless / receptor tyrosine kinase / RTK / drosophila / eye development / vision / photoreceptor / ROS1 / SIGNALING PROTEIN / bride of sevenless / boss / GPCR
Function / homology
Function and homology information


R8 cell-mediated photoreceptor organization / rhabdomere microvillus membrane / sevenless binding / germ-line stem-cell niche homeostasis / transmembrane receptor protein kinase activity / R7 cell fate commitment / sevenless signaling pathway / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / lipid homeostasis / response to glucose ...R8 cell-mediated photoreceptor organization / rhabdomere microvillus membrane / sevenless binding / germ-line stem-cell niche homeostasis / transmembrane receptor protein kinase activity / R7 cell fate commitment / sevenless signaling pathway / adenylate cyclase inhibiting G protein-coupled glutamate receptor activity / lipid homeostasis / response to glucose / transmembrane receptor protein tyrosine kinase activity / visual perception / placental growth factor receptor activity / insulin receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / GPI-linked ephrin receptor activity / transmembrane-ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / cell surface receptor protein tyrosine kinase signaling pathway / glucose homeostasis / histone H3Y41 kinase activity / histone H2AXY142 kinase activity / receptor complex / receptor ligand activity / ATP binding / plasma membrane
Similarity search - Function
Bride of sevenless protein / : / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Six-bladed beta-propeller, TolB-like / Fibronectin type III domain ...Bride of sevenless protein / : / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Six-bladed beta-propeller, TolB-like / Fibronectin type III domain / : / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Protein sevenless / Protein bride of sevenless
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 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-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44503.png

Downloads & links

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Map

FileDownload / File: emd_44503.map.gz / Format: CCP4 / Size: 244.1 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 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. Å		0.83 Å/pix.
x 400 pix.
= 332. 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: 0.7
Minimum - Maximum-3.6001854 - 7.272342
Average (Standard dev.)0.002811174 (±0.07030062)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_44503_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44503_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44503_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Sevenless extracellular domain in complex with Bride of Sevenless...

EntireName: Sevenless extracellular domain in complex with Bride of Sevenless extracellular domain
Components
  • Complex: Sevenless extracellular domain in complex with Bride of Sevenless extracellular domain
    • Protein or peptide: Protein sevenless
    • Protein or peptide: Protein bride of sevenless
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Sevenless extracellular domain in complex with Bride of Sevenless...

SupramoleculeName: Sevenless extracellular domain in complex with Bride of Sevenless extracellular domain
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Protein sevenless

MacromoleculeName: Protein sevenless / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 225.292922 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: DVCRSHNYTV HQSPEPVSKD QMRLLRPKLD SDVVEKVAIW HKHAAAAPPS IVEGIAISSR PQSTMAHHPD DRDRDRDPSE EQHGVDERM VLERVTRDCV QRCIVEEDLF LDEFGIQCEK ADNGEKCYKT RCTKGCAQWY RALKELESCQ EACLSLQFYP Y DMPCIGAC ...String:
DVCRSHNYTV HQSPEPVSKD QMRLLRPKLD SDVVEKVAIW HKHAAAAPPS IVEGIAISSR PQSTMAHHPD DRDRDRDPSE EQHGVDERM VLERVTRDCV QRCIVEEDLF LDEFGIQCEK ADNGEKCYKT RCTKGCAQWY RALKELESCQ EACLSLQFYP Y DMPCIGAC EMAQRDYWHL QRLAISHLVE RTQPQLERAP RADGQSTPLT IRWAMHFPEH YLASRPFNIQ YQFVDHHGEE LD LEQEDQD ASGETGSSAW FNLADYDCDE YYVCEILEAL IPYTQYRFRF ELPFGENRDE VLYSPATPAY QTPPEGAPIS APV IEHLMG LDDSHLAVHW HPGRFTNGPI EGYRLRLSSS EGNATSEQLV PAGRGSYIFS QLQAGTNYTL ALSMINKQGE GPVA KGFVQ THSARNEKPA KDLTESVLLV GRRAVMWQSL EPAGENSMIY QSQEELADIA WSKREQQLWL LNVHGELRSL KFESG QMVS PAQQLKLDLG NISSGRWVPR RLSFDWLHHR LYFAMESPER NQSSFQIIST DLLGESAQKV GESFDLPVEQ LEVDAL NGW IFWRNEESLW RQDLHGRMIH RLLRIRQPGW FLVQPQHFII HLMLPQEGKF LEISYDGGFK HPLPLPPPSN GAGNGPA SS HWQSFALLGR SLLLPDSGQL ILVEQQGQAA SPSASWPLKN LPDCWAVILL VPESQPLTSA GGKPHSLKAL LGAQAAKI S WKEPERNPYQ SADAARSWSY ELEVLDVASQ SAFSIRNIRG PIFGLQRLQP DNLYQLRVRA INVDGEPGEW TEPLAARTW PLGPHRLRWA SRQGSVIHTN ELGEGLEVQQ EQLERLPGPM TMVNESVGYY VTGDGLLHCI NLVHSQWGCP ISEPLQHVGS VTYDWRGGR VYWTDLARNC VVRMDPWSGS RELLPVFEAN FLALDPRQGH LYYATSSQLS RHGSTPDEAV TYYRVNGLEG S IASFVLDT QQDQLFWLVK GSGALRLYRA PLTAGGDSLQ MIQQIKGVFQ AVPDSLQLLR PLGALLWLER SGRRARLVRL AA PLDVMEL PTPDQASPAS ALQLLDPQPL PPRDEGVIPM TVLPDSVRLD DGHWDDFHVR WQPSTSGGNH SVSYRLLLEF GQR LQTLDL STPFARLTQL PQAQLQLKIS ITPRTAWRSG DTTRVQLTTP PVAPSQPRRL RVFVERLATA LQEANVSAVL RWDA PEQGQ EAPMQALEYH ISCWVGSELH EELRLNQSAL EARVEHLQPD QTYHFQVEAR VAATGAAAGA ASHALHVAPE VQAVP RVLY ANAEFIGELD LDTRNRRRLV HTASPVEHLV GIEGEQRLLW VNEHVELLTH VPGSAPAKLA RMRAEVLALA VDWIQR IVY WAELDATAPQ AAIIYRLDLC NFEGKILQGE RVWSTPRGRL LKDLVALPQA QSLIWLEYEQ GSPRNGSLRG RNLTDGS EL EWATVQPLIR LHAGSLEPGS ETLNLVDNQG KLCVYDVARQ LCTASALRAQ LNLLGEDSIA GQLAQDSGYL YAVKNWSI R AYGRRRQQLE YTVELEPEEV RLLQAHNYQA YPPKNCLLLP SSGGSLLKAT DCEEQRCLLN LPMITASEDC PLPIPGVRY QLNLTLARGP GSEEHDHGVE PLGQWLLGAG ESLNLTDLLP FTRYRVSGIL SSFYQKKLAL PTLVLAPLEL LTASATPSPP RNFSVRVLS PRELEVSWLP PEQLRSESVY YTLHWQQELD GENVQDRREW EAHERRLETA GTHRLTGIKP GSGYSLWVQA H ATPTKSNS SERLHVRSFA ELPELQLLEL GPYSLSLTWA GTPDPLGSLQ LECRSSAEQL RRNVAGNHTK MVVEPLQPRT RY QCRLLLG YAATPGAPLY HGTAEVYETL GDAPSQPGKP QLEHIAEEVF RVTWTAARGN GAPIALYNLE ALQARSDINS GGS LEQLPW AEEPVVVEDQ WLDFCNTTEL SCIVKSLHSS RLLLFRVRAR SLEHGWGPYS EESERVAEPF VSHHHHHHWS HPQF EK

UniProtKB: Protein sevenless

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Macromolecule #2: Protein bride of sevenless

MacromoleculeName: Protein bride of sevenless / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 5 / 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

Startup modelType of model: INSILICO MODEL / In silico model: Alphafold prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 381423
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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