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- PDB-9ozh: Cryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformat... -

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Basic information

Entry
Database: PDB / ID: 9ozh
TitleCryo-EM structure of 1:2:1 ROS1/NEL/NICOL holo-complex, conformation 2.
Components
  • NELL2-interacting cell ontogeny regulator 1
  • Protein NEL
  • Tyrosine-protein kinase receptor
KeywordsSIGNALING PROTEIN / ROS1 / NEL
Function / homology
Function and homology information


negative regulation of retinal ganglion cell axon guidance / columnar/cuboidal epithelial cell development / regulation of phosphate transport / transferrin receptor binding / regulation of TOR signaling / commissural neuron axon guidance / fertilization / neural crest cell migration / 3'-UTR-mediated mRNA stabilization / positive regulation of cell division ...negative regulation of retinal ganglion cell axon guidance / columnar/cuboidal epithelial cell development / regulation of phosphate transport / transferrin receptor binding / regulation of TOR signaling / commissural neuron axon guidance / fertilization / neural crest cell migration / 3'-UTR-mediated mRNA stabilization / positive regulation of cell division / regulation of ERK1 and ERK2 cascade / transmembrane receptor protein tyrosine kinase activity / positive regulation of neuron differentiation / cell surface receptor protein tyrosine kinase signaling pathway / protein kinase C binding / mRNA 3'-UTR binding / receptor protein-tyrosine kinase / heparin binding / gene expression / protein phosphatase binding / spermatogenesis / cell population proliferation / receptor complex / negative regulation of gene expression / calcium ion binding / perinuclear region of cytoplasm / cell surface / extracellular space / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Neuropeptide-like protein / Neuropeptide-like / : / 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 ...Neuropeptide-like protein / Neuropeptide-like / : / 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 / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / 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
Tyrosine-protein kinase receptor / NELL2-interacting cell ontogeny regulator 1 / Protein NEL
Similarity search - Component
Biological speciesGallus gallus (chicken)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsAn, W.D. / Zhang, X.W. / Bai, X.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural Basis for the Activation of the Vertebrate ROS1 Receptor by the NEL/NICOL Ligand Complex
Authors: An, W.D. / Zhang, X.W. / Bai, X.C.
History
DepositionJun 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Protein NEL
C: Protein NEL
A: NELL2-interacting cell ontogeny regulator 1
D: Tyrosine-protein kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,39036
Polymers453,4994
Non-polymers7,89132
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Protein NEL / 93 kDa protein


Mass: 91070.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: NEL / Production host: Homo sapiens (human) / References: UniProt: Q90827
#2: Protein NELL2-interacting cell ontogeny regulator 1 / NELL2-interacting cofactor for lumicrine signaling / NICOL


Mass: 10182.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NICOL1, C4orf48 / Production host: Homo sapiens (human) / References: UniProt: Q5BLP8
#3: Protein Tyrosine-protein kinase receptor


Mass: 261174.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ROS1 / Production host: Homo sapiens (human)
References: UniProt: F1NQL9, receptor protein-tyrosine kinase
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 1:2:1 complex between chicken ROS1, chicken NEL and human NICOL
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Gallus gallus (chicken)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
2SerialEMimage acquisition
4GctfCTF correction
9PHENIX1.21.1_5286model refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16841 / Symmetry type: POINT
RefinementHighest resolution: 4.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00226693
ELECTRON MICROSCOPYf_angle_d0.56336257
ELECTRON MICROSCOPYf_dihedral_angle_d12.32610259
ELECTRON MICROSCOPYf_chiral_restr0.0434071
ELECTRON MICROSCOPYf_plane_restr0.0044676

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