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- EMDB-75151: Cryo-EM structure of Receptor Tyrosine Kinase ROS1 in complex wit... -

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Basic information

Entry
Database: EMDB / ID: EMD-75151
TitleCryo-EM structure of Receptor Tyrosine Kinase ROS1 in complex with Fab-RX5
Map datahalf map A
Sample
  • Complex: Receptor tyrosine kinase ROS1 in complex with Fab-RX5
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase ROS
    • Protein or peptide: Fab-RX5 light chain
    • Protein or peptide: Fab-RX5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsReceptor tyrosine kinase / ROS1 extracellular bent-over conformation / Inhibitory Fab-RX5 / TRANSFERASE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


columnar/cuboidal epithelial cell development / regulation of phosphate transport / regulation of TOR signaling / regulation of ERK1 and ERK2 cascade / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell growth / receptor protein-tyrosine kinase / protein tyrosine kinase activity / gene expression ...columnar/cuboidal epithelial cell development / regulation of phosphate transport / regulation of TOR signaling / regulation of ERK1 and ERK2 cascade / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell growth / receptor protein-tyrosine kinase / protein tyrosine kinase activity / gene expression / protein phosphatase binding / spermatogenesis / cell differentiation / protein phosphorylation / receptor complex / negative regulation of gene expression / perinuclear region of cytoplasm / cell surface / signal transduction / ATP binding / plasma membrane
Similarity search - Function
LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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 ...LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / 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
Proto-oncogene tyrosine-protein kinase ROS
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsLi H / Klein D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Clustering and a conformational switch drive activation of the mammalian receptor tyrosine kinase ROS1
Authors: Li H / Klein D
History
DepositionJan 19, 2026-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75151.png

Downloads & links

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Map

FileDownload / File: emd_75151.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhalf map A
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å		0.83 Å/pix.
x 480 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.89465207 - 1.3679374
Average (Standard dev.)-0.00013553018 (±0.022288047)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_75151_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_75151_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Receptor tyrosine kinase ROS1 in complex with Fab-RX5

EntireName: Receptor tyrosine kinase ROS1 in complex with Fab-RX5
Components
  • Complex: Receptor tyrosine kinase ROS1 in complex with Fab-RX5
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase ROS
    • Protein or peptide: Fab-RX5 light chain
    • Protein or peptide: Fab-RX5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Receptor tyrosine kinase ROS1 in complex with Fab-RX5

SupramoleculeName: Receptor tyrosine kinase ROS1 in complex with Fab-RX5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Proto-oncogene tyrosine-protein kinase ROS

MacromoleculeName: Proto-oncogene tyrosine-protein kinase ROS / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: receptor protein-tyrosine kinase
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 112.553805 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: STVLSSCLTS CVTNLGRQLD SGTRYNLSEA CIHGCQFWNS VDQETCALKC NDTYATICER ESCEVGCSNA EGSYEEEVLE STELPTAPF ASSIGSHGVT LRWNPANISG VKYIIQWKYA QLPGSWTFTE TVSKLSYTVE PLHPFTEYIF RVVWIFTAQL H LYSPPSPS ...String:
STVLSSCLTS CVTNLGRQLD SGTRYNLSEA CIHGCQFWNS VDQETCALKC NDTYATICER ESCEVGCSNA EGSYEEEVLE STELPTAPF ASSIGSHGVT LRWNPANISG VKYIIQWKYA QLPGSWTFTE TVSKLSYTVE PLHPFTEYIF RVVWIFTAQL H LYSPPSPS YRTHPYGVPE TAPLILNMES WSPDTVEVSW APPHFPGGPI LGYNLRLISK NQKLDSGTQR TSFQFYSTLP NT TYRFSIA AVNEVGEGPE AESTVTTPSP SVQEEEQWLF LSRKTSLRKR SLKYLVDEAH CLWSDAIHHN ITGISVYAQQ QVV YFSEGT VIWMKGAANM SDVSDLRIFY QGSGLVSSIS IDWLYQRMYF IMDKLVYVCE LKNCSNLEEI TPFSLIAPQK VVVD SYNGY LFYLLRDGIY RVNLPLPSGR DTKAVRIVES GTLKDFAVKP QSKRIIYFND TMQLFMSTFL DGSAFHRVLP WVPLV TVKS FACENNDFLI TDGKAIFQQD SLSFNEFIVG CDLSHIEEFG FGNLVIFGSS VQSYPLPGHP QEVSVLFGSR EALIQW TPP ALAIGASPSA WQNWTYEVKV YSQDILEITQ VFSNISGTML NVPELQSSTK YTVSVRASSP KGPGPWSAPS VGTTLVP AT EPPFIMAVKE DGLWSKPLCS FGPGEFLSSD VGNVSDMDWY NNSLYYSDTK GNVYVRPLNG MDISENYHIP SIVGAGAL A FEWLGHFLYW AGKTYVIQRQ SVLTGHTDIV THVKLLVNDM AVDSVGGYLY WTTLYSVEST RLNGESSLVL QAQPWLSGK KVIALTLDLS DGLLYWLVQD NQCIHLYTAV LRGWSGGDAT ITEFAAWSTS EISQNALMYY SGRLFWINGF RIITAQEIGQ RTSVSVSEP AKFNQFTIIQ TSLKPLPGNF SSTPKVIPDP VQESSFRIEG HTSSFQILWN EPPAVDWGIV FYSVEFSTHS K FLIIEQQS LPIFTVEGLE PYTLFNLSVT PYTYWGKGQK TSLSFRAP

UniProtKB: Proto-oncogene tyrosine-protein kinase ROS

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Macromolecule #2: Fab-RX5 light chain

MacromoleculeName: Fab-RX5 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.079678 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SMASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGSR SGTDFTLTIS SLQPEDFAT YYCQQYYAYS LFTFGQGTKV EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
SMASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGSR SGTDFTLTIS SLQPEDFAT YYCQQYYAYS LFTFGQGTKV EIKRTVAAPS VFIFPPSDSQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE CGGSDYKDDD DK

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Macromolecule #3: Fab-RX5 heavy chain

MacromoleculeName: Fab-RX5 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.503346 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: EISEVQLVES GGGLVQPGGS LRLSCAASGF NLSSSSMHWV RQAPGKGLEW VAYIYPYSSS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSYWGYYGL DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
EISEVQLVES GGGLVQPGGS LRLSCAASGF NLSSSSMHWV RQAPGKGLEW VAYIYPYSSS TSYADSVKGR FTISADTSKN TAYLQMNSL RAEDTAVYYC ARSYWGYYGL DYWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSCDKT HTSRHHHHHH

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 166992
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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