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- EMDB-71938: Cryo-EM structure of receptor tyrosine kinase ROS1 extracellular ... -

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Basic information

Entry
Database: EMDB / ID: EMD-71938
TitleCryo-EM structure of receptor tyrosine kinase ROS1 extracellular domain in complex with NELL2
Map dataEM map
Sample
  • Complex: Receptor tyrosine kinase ROS1 extracellular domain in complex with NELL2
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase ROS
    • Protein or peptide: Protein kinase C-binding protein NELL2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsReceptor tyrosine kinase ROS1 / ROS1-NELL2 complex / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


columnar/cuboidal epithelial cell development / regulation of phosphate transport / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of TOR signaling / commissural neuron axon guidance / fertilization / regulation of ERK1 and ERK2 cascade / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / protein kinase C binding ...columnar/cuboidal epithelial cell development / regulation of phosphate transport / Regulation of commissural axon pathfinding by SLIT and ROBO / regulation of TOR signaling / commissural neuron axon guidance / fertilization / regulation of ERK1 and ERK2 cascade / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / protein kinase C binding / regulation of cell growth / receptor protein-tyrosine kinase / neuron cellular homeostasis / heparin binding / protein tyrosine kinase activity / gene expression / protein phosphatase binding / spermatogenesis / cell differentiation / protein phosphorylation / receptor complex / negative regulation of gene expression / calcium ion binding / perinuclear region of cytoplasm / cell surface / signal transduction / extracellular space / extracellular region / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / EGF domain / EGF domain / : / Thrombospondin N-terminal -like domains. / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. ...: / EGF domain / EGF domain / : / Thrombospondin N-terminal -like domains. / Laminin G domain / von Willebrand factor (vWF) type C domain / von Willebrand factor type C domain / VWFC domain signature. / VWFC domain profile. / Laminin G domain / Laminin G domain / von Willebrand factor (vWF) type C domain / VWFC domain / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Six-bladed beta-propeller, TolB-like / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Fibronectin type III domain / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like 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 / Concanavalin A-like lectin/glucanase domain superfamily / 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 / Protein kinase C-binding protein NELL2
Similarity search - Component
Biological speciesMus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.45 Å
AuthorsLi H / Klein D
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis for regulation of the receptor tyrosine kinase ROS1
Authors: Li H / Klein D
History
DepositionAug 5, 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_71938.png

Downloads & links

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Map

FileDownload / File: emd_71938.map.gz / Format: CCP4 / Size: 1000 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.)
0.83 Å/pix.
x 640 pix.
= 532.48 Å		0.83 Å/pix.
x 640 pix.
= 532.48 Å		0.83 Å/pix.
x 640 pix.
= 532.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0248
Minimum - Maximum-0.31606022 - 0.47808942
Average (Standard dev.)-0.00017500525 (±0.007010312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 532.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_71938_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_71938_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 in complex wit...

EntireName: Receptor tyrosine kinase ROS1 extracellular domain in complex with NELL2
Components
  • Complex: Receptor tyrosine kinase ROS1 extracellular domain in complex with NELL2
    • Protein or peptide: Proto-oncogene tyrosine-protein kinase ROS
    • Protein or peptide: Protein kinase C-binding protein NELL2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Receptor tyrosine kinase ROS1 extracellular domain in complex wit...

SupramoleculeName: Receptor tyrosine kinase ROS1 extracellular domain in complex with NELL2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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: 207.672344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: TVLSSCLTSC VTNLGRQLDS GTRYNLSEAC IHGCQFWNSV DQETCALKCN DTYATICERE SCEVGCSNAE GSYEEEVLES TELPTAPFA SSIGSHGVTL RWNPANISGV KYIIQWKYAQ LPGSWTFTET VSKLSYTVEP LHPFTEYIFR VVWIFTAQLH L YSPPSPSY ...String:
TVLSSCLTSC VTNLGRQLDS GTRYNLSEAC IHGCQFWNSV DQETCALKCN DTYATICERE SCEVGCSNAE GSYEEEVLES TELPTAPFA SSIGSHGVTL RWNPANISGV KYIIQWKYAQ LPGSWTFTET VSKLSYTVEP LHPFTEYIFR VVWIFTAQLH L YSPPSPSY RTHPYGVPET APLILNMESW SPDTVEVSWA PPHFPGGPIL GYNLRLISKN QKLDSGTQRT SFQFYSTLPN TT YRFSIAA VNEVGEGPEA ESTVTTPSPS VQEEEQWLFL SRKTSLRKRS LKYLVDEAHC LWSDAIHHNI TGISVYAQQQ VVY FSEGTV IWMKGAANMS DVSDLRIFYQ GSGLVSSISI DWLYQRMYFI MDKLVYVCEL KNCSNLEEIT PFSLIAPQKV VVDS YNGYL FYLLRDGIYR VNLPLPSGRD TKAVRIVESG TLKDFAVKPQ SKRIIYFNDT MQLFMSTFLD GSAFHRVLPW VPLVT VKSF ACENNDFLIT DGKAIFQQDS LSFNEFIVGC DLSHIEEFGF GNLVIFGSSV QSYPLPGHPQ EVSVLFGSRE ALIQWT PPA LAIGASPSAW QNWTYEVKVY SQDILEITQV FSNISGTMLN VPELQSSTKY TVSVRASSPK GPGPWSAPSV GTTLVPA TE PPFIMAVKED GLWSKPLCSF GPGEFLSSDV GNVSDMDWYN NSLYYSDTKG NVYVRPLNGM DISENYHIPS IVGAGALA F EWLGHFLYWA GKTYVIQRQS VLTGHTDIVT HVKLLVNDMA VDSVGGYLYW TTLYSVESTR LNGESSLVLQ AQPWLSGKK VIALTLDLSD GLLYWLVQDN QCIHLYTAVL RGWSGGDATI TEFAAWSTSE ISQNALMYYS GRLFWINGFR IITAQEIGQR TSVSVSEPA KFNQFTIIQT SLKPLPGNFS STPKVIPDPV QESSFRIEGH TSSFQILWNE PPAVDWGIVF YSVEFSTHSK F LIIEQQSL PIFTVEGLEP YTLFNLSVTP YTYWGKGQKT SLSFRAPESV PSAPENPRIF ILSSGRYTKK NEVVVEFRWN KP KHENGVL TKFEIFYHIS KQSGTNRSTE DWMSASVIPP VMSFQLEAVS PEYTVAFQVR VFTSKGPGPF SDIVMSKTSE IKP CPYLIS LLGNKIVFLD MDQNQVLWTF SLEGDVSTVG YTTDDEMGYF AQGDTLFLLN LRNHSSSKLF QDALVSDIRV IAVD WIARH LYFALKASQN GTQIFNVDLE HKVKSPREVK TCKAHTTIIS FSIYPLLSRL YWTEVSDLGH QMFYCNISNH TSQHV LQPK ASNQHGRSQC SCNVTESELS GAMTVDTSDP DRPWIYFTKR QEIWAMDLEG CQCWKVIMVP TIPGKRIISL TVDGEF IYW IMKTKDDAQI YQAKKGSGAI LSQVKASRSK HILAYSSALQ PFPDKAYLSL ASDMVEATIL YATNTSLTLK LPPVKTN LT WHGITHPTST YLIYYMEANR ANSSDRRHKM LESQENVARI EGLQPFSMYM IQIAVKNYYS EPLEHLPLGK EIQGQTKS G VPGAVCHINA TVLSDTSLHV FWTESHKPNG PKESVRYQLV MSYLAPIPET PLRQGEFPSA KLSLLITKLS GGQLYVMKV LACHPEEMWC TESHPVSVNM FDTPEKPSAL VPENTSLQLD WKARSNVNLT GFWFELQKWK YNEFYHVKAS CSQGPVYVCN ITDLQPYTS YNIRVVVVYT TGENSSSIPE SFKTKAGVPS KPGIPKLLEG SKNSIQWEKA EDNGSRLMYY TLEVRKGISN D SQNQSSRW KVVFNGSCSS ICTWRSKNLK GTFQFRAVAA NEIGLGEYSE ISEDITLVED GGGGSSAWSH PQFEKGGGSG GG SGGSAWS HPQFEK

UniProtKB: Proto-oncogene tyrosine-protein kinase ROS

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Macromolecule #2: Protein kinase C-binding protein NELL2

MacromoleculeName: Protein kinase C-binding protein NELL2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 92.446148 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LGVDPSLQID VLTELELGES TTGVRQVPGL HNGTKAFLFQ DTPRSIKAST ATAEQFFQKL RNKHEFTILV TLKQTHLNSG VILSIHHLD HRYLELESSG HRNEVRLHYR SGSHRPHTEV FPYILADDKW HKLSLAISAS HLILHIDCNK IYERVVEKPS T DLPLGTTF ...String:
LGVDPSLQID VLTELELGES TTGVRQVPGL HNGTKAFLFQ DTPRSIKAST ATAEQFFQKL RNKHEFTILV TLKQTHLNSG VILSIHHLD HRYLELESSG HRNEVRLHYR SGSHRPHTEV FPYILADDKW HKLSLAISAS HLILHIDCNK IYERVVEKPS T DLPLGTTF WLGQRNNAHG YFKGIMQDVQ LLVMPQGFIA QCPDLNRTCP TCNDFHGLVQ KIMELQDILA KTSAKLSRAE QR MNRLDQC YCERTCTMKG TTYREFESWI DGCKNCTCLN GTIQCETLIC PNPDCPLKSA LAYVDGKCCK ECKSICQFQG RTY FEGERN TVYSSSGVCV LYECKDQTMK LVESSGCPAL DCPESHQITL SHSCCKVCKG YDFCSERHNC MENSICRNLN DRAV CSCRD GFRALREDNA YCEDIDECAE GRHYCRENTM CVNTPGSFMC ICKTGYIRID DYSCTEHDEC ITNQHNCDEN ALCFN TVGG HNCVCKPGYT GNGTTCKAFC KDGCRNGGAC IAANVCACPQ GFTGPSCETD IDECSDGFVQ CDSRANCINL PGWYHC ECR DGYHDNGMFS PSGESCEDID ECGTGRHSCA NDTICFNLDG GYDCRCPHGK NCTGDCIHDG KVKHNGQIWV LENDRCS VC SCQNGFVMCR RMVCDCENPT VDLFCCPECD PRLSSQCLHQ NGETLYNSGD TWVQNCQQCR CLQGEVDCWP LPCPDVEC E FSILPENECC PRCVTDPCQA DTIRNDITKT CLDEMNVVRF TGSSWIKHGT ECTLCQCKNG HICCSVDPQC LQELGGGGS SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK

UniProtKB: Protein kinase C-binding protein NELL2

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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: 10 / 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: 4.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 59436
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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