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- EMDB-44502: Cryo-EM structure of Sevenless extracellular domain (monomer) -

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Basic information

Entry
Database: EMDB / ID: EMD-44502
TitleCryo-EM structure of Sevenless extracellular domain (monomer)
Map dataSharpened map
Sample
  • Organelle or cellular component: Sevenless extracellular domain
    • Protein or peptide: Protein sevenless
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordssevenless / receptor tyrosine kinase / RTK / drosophila / eye development / vision / photoreceptor / ROS1 / SIGNALING PROTEIN
Function / homology
Function and homology information


germ-line stem-cell niche homeostasis / transmembrane receptor protein kinase activity / R7 cell fate commitment / sevenless signaling pathway / regulation of TOR signaling / transmembrane receptor protein tyrosine kinase activity / visual perception / cell surface receptor protein tyrosine kinase signaling pathway / placental growth factor receptor activity / insulin receptor activity ...germ-line stem-cell niche homeostasis / transmembrane receptor protein kinase activity / R7 cell fate commitment / sevenless signaling pathway / regulation of TOR signaling / transmembrane receptor protein tyrosine kinase activity / visual perception / cell surface receptor protein tyrosine kinase signaling pathway / 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 / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / receptor complex / ATP binding / plasma membrane
Similarity search - Function
LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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 ...LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 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_44502.png

Downloads & links

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Map

FileDownload / File: emd_44502.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 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: 0.4
Minimum - Maximum-1.5951139 - 3.2090523
Average (Standard dev.)-0.0005447833 (±0.046101414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_44502_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44502_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44502_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Sevenless extracellular domain

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

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Supramolecule #1: Sevenless extracellular domain

SupramoleculeName: 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 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 #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / 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: 8
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: INSILICO MODEL / In silico model: Alphafold prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1173833
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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