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- EMDB-71895: Cryo-EM structure of receptor tyrosine kinase ROS1 extracellular ... -

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Basic information

Entry
Database: EMDB / ID: EMD-71895
TitleCryo-EM structure of receptor tyrosine kinase ROS1 extracellular domain
Map dataem map
Sample
  • Complex: Receptor tyrosine kinase ROS1 extracellular domain
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase ROS
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsReceptor tyrosine kinase ROS1 / ROS1-NELL2 complex / TRANSFERASE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.57 Å
AuthorsLi H / Klein D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Structural basis for regulation of the receptor tyrosine kinase ROS1
Authors: Li H / Klein D
History
DepositionAug 3, 2025-
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_71895.png

Downloads & links

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Map

FileDownload / File: emd_71895.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 384 pix.
= 499.2 Å		1.3 Å/pix.
x 384 pix.
= 499.2 Å		1.3 Å/pix.
x 384 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0857
Minimum - Maximum-0.38687935 - 0.8949566
Average (Standard dev.)-0.00032718942 (±0.014786816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 499.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_71895_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_71895_half_map_2.map
Annotationhalf 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 : Receptor tyrosine kinase ROS1 extracellular domain

EntireName: Receptor tyrosine kinase ROS1 extracellular domain
Components
  • Complex: Receptor tyrosine kinase ROS1 extracellular domain
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase ROS
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Receptor tyrosine kinase ROS1 extracellular domain

SupramoleculeName: Receptor tyrosine kinase ROS1 extracellular domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 207.759422 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 TSLSFRAPES VPSAPENPRI FILSSGRYTK KNEVVVEFRW NK PKHENGV LTKFEIFYHI SKQSGTNRST EDWMSASVIP PVMSFQLEAV SPEYTVAFQV RVFTSKGPGP FSDIVMSKTS EIK PCPYLI SLLGNKIVFL DMDQNQVLWT FSLEGDVSTV GYTTDDEMGY FAQGDTLFLL NLRNHSSSKL FQDALVSDIR VIAV DWIAR HLYFALKASQ NGTQIFNVDL EHKVKSPREV KTCKAHTTII SFSIYPLLSR LYWTEVSDLG HQMFYCNISN HTSQH VLQP KASNQHGRSQ CSCNVTESEL SGAMTVDTSD PDRPWIYFTK RQEIWAMDLE GCQCWKVIMV PTIPGKRIIS LTVDGE FIY WIMKTKDDAQ IYQAKKGSGA ILSQVKASRS KHILAYSSAL QPFPDKAYLS LASDMVEATI LYATNTSLTL KLPPVKT NL TWHGITHPTS TYLIYYMEAN RANSSDRRHK MLESQENVAR IEGLQPFSMY MIQIAVKNYY SEPLEHLPLG KEIQGQTK S GVPGAVCHIN ATVLSDTSLH VFWTESHKPN GPKESVRYQL VMSYLAPIPE TPLRQGEFPS AKLSLLITKL SGGQLYVMK VLACHPEEMW CTESHPVSVN MFDTPEKPSA LVPENTSLQL DWKARSNVNL TGFWFELQKW KYNEFYHVKA SCSQGPVYVC NITDLQPYT SYNIRVVVVY TTGENSSSIP ESFKTKAGVP SKPGIPKLLE GSKNSIQWEK AEDNGSRLMY YTLEVRKGIS N DSQNQSSR WKVVFNGSCS SICTWRSKNL KGTFQFRAVA ANEIGLGEYS EISEDITLVE DGGGGSSAWS HPQFEKGGGS GG GSGGSAW SHPQFEK

UniProtKB: Proto-oncogene tyrosine-protein kinase ROS

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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: 11 / 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: 4.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 23490
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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