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- PDB-9xzg: Cryo-EM structure of ALK in complex with CRBN/DDB1 and TRI-611 -

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Basic information

Entry
Database: PDB / ID: 9xzg
TitleCryo-EM structure of ALK in complex with CRBN/DDB1 and TRI-611
Components
  • ALK tyrosine kinase receptor
  • Protein cereblon
KeywordsLIGASE / DNA Binding Protein-Transferase Complex / DNA BINDING PROTEIN / Ternary Complex / Molecular Glue
Function / homology
Function and homology information


ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / negative regulation of monoatomic ion transmembrane transport ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / negative regulation of monoatomic ion transmembrane transport / ALK mutants bind TKIs / phosphorylation / positive regulation of dendrite development / peptidyl-tyrosine autophosphorylation / regulation of neuron differentiation / Signaling by ALK / energy homeostasis / locomotory exploration behavior / Cul4A-RING E3 ubiquitin ligase complex / neuron development / limb development / negative regulation of lipid catabolic process / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of protein-containing complex assembly / receptor protein-tyrosine kinase / Signaling by ALK fusions and activated point mutants / regulation of cell population proliferation / protein autophosphorylation / heparin binding / protein tyrosine kinase activity / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / transmembrane transporter binding / signaling receptor complex / protein ubiquitination / perinuclear region of cytoplasm / signal transduction / protein-containing complex / extracellular exosome / ATP binding / membrane / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. ...: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / LDL receptor-like superfamily / PUA-like 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Protein cereblon / ALK tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsBart, A.G. / Kamadurai, H.B.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of ALK in complex with CRBN/DDB1 and TRI-611
Authors: Bart, A.G. / Kamadurai, H.B.
History
DepositionAug 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 5, 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

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Assembly

Deposited unit
B: Protein cereblon
C: ALK tyrosine kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2954
Polymers86,8252
Non-polymers4702
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein cereblon


Mass: 50690.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96SW2
#2: Protein ALK tyrosine kinase receptor / Anaplastic lymphoma kinase


Mass: 36134.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UM73, receptor protein-tyrosine kinase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-A1CRM / (3S)-3-{2-oxo-5-[(3-phenyl-1,2,4-oxadiazol-5-yl)methyl]-1,3-benzoxazol-3(2H)-yl}piperidine-2,6-dione


Mass: 404.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16N4O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Ternary complex of ALK with CRBN/DDB1 and TRI-611 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
12RELION3D reconstruction
19Servalcat0.4.105model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 345494 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8d7v

8d7v


Accession code: 8d7v / Source name: PDB / Type: experimental model

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