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- EMDB-44508: Cryo-EM reconstruction of Sev extracellular domain (dimer, global... -

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Basic information

Entry
Database: EMDB / ID: EMD-44508
TitleCryo-EM reconstruction of Sev extracellular domain (dimer, global refinement, pH 4.6)
Map dataSharpened map
Sample
  • Organelle or cellular component: Sevenless extracellular domain
    • Protein or peptide: Sevenless
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 / boss receptor activity / transmembrane receptor protein tyrosine kinase activity / visual perception / cell surface receptor protein tyrosine kinase signaling pathway / receptor protein-tyrosine kinase ...germ-line stem-cell niche homeostasis / transmembrane receptor protein kinase activity / R7 cell fate commitment / sevenless signaling pathway / regulation of TOR signaling / boss receptor activity / transmembrane receptor protein tyrosine kinase activity / visual perception / cell surface receptor protein tyrosine kinase signaling pathway / 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: 3.67 Å
AuthorsCerutti G / Shapiro L
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Cryo-EM reconstruction of Sev extracellular domain (dimer, global refinement, pH 4.6)
Authors: Cerutti G / Shapiro L
History
DepositionApr 18, 2024-
Header (metadata) releaseMay 7, 2025-
Map releaseMay 7, 2025-
UpdateMay 7, 2025-
Current statusMay 7, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44508.png

Downloads & links

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Map

FileDownload / File: emd_44508.map.gz / Format: CCP4 / Size: 600.7 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 540 pix.
= 448.2 Å		0.83 Å/pix.
x 540 pix.
= 448.2 Å		0.83 Å/pix.
x 540 pix.
= 448.2 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: 0.26
Minimum - Maximum-0.7642587 - 1.4852842
Average (Standard dev.)-0.0003016655 (±0.040172417)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 448.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_44508_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_44508_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44508_half_map_2.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 : Sevenless extracellular domain

EntireName: Sevenless extracellular domain
Components
  • Organelle or cellular component: Sevenless extracellular domain
    • Protein or peptide: Sevenless

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Supramolecule #1: Sevenless extracellular domain

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

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Macromolecule #1: Sevenless

MacromoleculeName: Sevenless / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: DVCRSHNYTV HQSPEPVSKD QMRLLRPKLD SDVVEKVAIW HKHAAAAPPS IVEGIAIS S RPQSTMAHHP DDRDRDRDPS EEQHGVDERM VLERVTRDCV QRCIVEEDLF LDEFGIQCE KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC ...String:
DVCRSHNYTV HQSPEPVSKD QMRLLRPKLD SDVVEKVAIW HKHAAAAPPS IVEGIAIS S RPQSTMAHHP DDRDRDRDPS EEQHGVDERM VLERVTRDCV QRCIVEEDLF LDEFGIQCE KADNGEKCYK TRCTKGCAQW YRALKELESC QEACLSLQFY PYDMPCIGAC EMAQRDYWHL QRLAISHLV ERTQPQLERA PRADGQSTPL TIRWAMHFPE HYLASRPFNI QYQFVDHHGE E LDLEQEDQ DASGETGSSA WFNLADYDCD EYYVCEILEA LIPYTQYRFR FELPFGENRD EV LYSPATP AYQTPPEGAP ISAPVIEHLM GLDDSHLAVH WHPGRFTNGP IEGYRLRLSS SEG NATSEQ LVPAGRGSYI FSQLQAGTNY TLALSMINKQ GEGPVAKGFV QTHSARNEKP AKDL TESVL LVGRRAVMWQ SLEPAGENSM IYQSQEELAD IAWSKREQQL WLLNVHGELR SLKFE SGQM VSPAQQLKLD LGNISSGRWV PRRLSFDWLH HRLYFAMESP ERNQSSFQII STDLLG ESA QKVGESFDLP VEQLEVDALN GWIFWRNEES LWRQDLHGRM IHRLLRIRQP GWFLVQP QH FIIHLMLPQE GKFLEISYDG GFKHPLPLPP PSNGAGNGPA SSHWQSFALL GRSLLLPD S GQLILVEQQG QAASPSASWP LKNLPDCWAV ILLVPESQPL TSAGGKPHSL KALLGAQAA KISWKEPERN PYQSADAARS WSYELEVLDV ASQSAFSIRN IRGPIFGLQR LQPDNLYQLR VRAINVDGE PGEWTEPLAA RTWPLGPHRL RWASRQGSVI HTNELGEGLE VQQEQLERLP G PMTMVNES VGYYVTGDGL LHCINLVHSQ WGCPISEPLQ HVGSVTYDWR GGRVYWTDLA RN CVVRMDP WSGSRELLPV FEANFLALDP RQGHLYYATS SQLSRHGSTP DEAVTYYRVN GLE GSIASF VLDTQQDQLF WLVKGSGALR LYRAPLTAGG DSLQMIQQIK GVFQAVPDSL QLLR PLGAL LWLERSGRRA RLVRLAAPLD VMELPTPDQA SPASALQLLD PQPLPPRDEG VIPMT VLPD SVRLDDGHWD DFHVRWQPST SGGNHSVSYR LLLEFGQRLQ TLDLSTPFAR LTQLPQ AQL QLKISITPRT AWRSGDTTRV QLTTPPVAPS QPRRLRVFVE RLATALQEAN VSAVLRW DA PEQGQEAPMQ ALEYHISCWV GSELHEELRL NQSALEARVE HLQPDQTYHF QVEARVAA T GAAAGAASHA LHVAPEVQAV PRVLYANAEF IGELDLDTRN RRRLVHTASP VEHLVGIEG EQRLLWVNEH VELLTHVPGS APAKLARMRA EVLALAVDWI QRIVYWAELD ATAPQAAIIY RLDLCNFEG KILQGERVWS TPRGRLLKDL VALPQAQSLI WLEYEQGSPR NGSLRGRNLT D GSELEWAT VQPLIRLHAG SLEPGSETLN LVDNQGKLCV YDVARQLCTA SALRAQLNLL GE DSIAGQL AQDSGYLYAV KNWSIRAYGR RRQQLEYTVE LEPEEVRLLQ AHNYQAYPPK NCL LLPSSG GSLLKATDCE EQRCLLNLPM ITASEDCPLP IPGVRYQLNL TLARGPGSEE HDHG VEPLG QWLLGAGESL NLTDLLPFTR YRVSGILSSF YQKKLALPTL VLAPLELLTA SATPS PPRN FSVRVLSPRE LEVSWLPPEQ LRSESVYYTL HWQQELDGEN VQDRREWEAH ERRLET AGT HRLTGIKPGS GYSLWVQAHA TPTKSNSSER LHVRSFAELP ELQLLELGPY SLSLTWA GT PDPLGSLQLE CRSSAEQLRR NVAGNHTKMV VEPLQPRTRY QCRLLLGYAA TPGAPLYH G TAEVYETLGD APSQPGKPQL EHIAEEVFRV TWTAARGNGA PIALYNLEAL QARSDINSG GSLEQLPWAE EPVVVEDQWL DFCNTTELSC IVKSLHSSRL LLFRVRARSL EHGWGPYSEE SERVAEPFV SHHHHHHWSH PQFEK

UniProtKB: Protein sevenless

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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: 4.6
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: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55908
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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