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- PDB-7lrz: Structure of the Human ALK GRD -

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Basic information

Entry
Database: PDB / ID: 7lrz
TitleStructure of the Human ALK GRD
ComponentsALK tyrosine kinase receptor
KeywordsTRANSFERASE / glycine rich domain / neuroblastoma / cancer / oncogene / SIGNALING PROTEIN
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 / regulation of dopamine receptor signaling pathway ...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 / regulation of dopamine receptor signaling pathway / response to environmental enrichment / ALK mutants bind TKIs / swimming behavior / positive regulation of dendrite development / regulation of neuron differentiation / adult behavior / Signaling by ALK / neuron development / negative regulation of lipid catabolic process / energy homeostasis / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / hippocampus development / receptor protein-tyrosine kinase / Signaling by ALK fusions and activated point mutants / positive regulation of NF-kappaB transcription factor activity / heparin binding / regulation of cell population proliferation / regulation of apoptotic process / protein tyrosine kinase activity / protein autophosphorylation / receptor complex / phosphorylation / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Glycine rich protein / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Tyrosine-protein kinase, catalytic domain ...Glycine rich protein / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Concanavalin A-like lectin/glucanase domain superfamily / Tyrosine-protein kinase, active site / 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
ALK tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsStayrook, S. / Li, T. / Klein, D.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)K22 CA215821 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA248532 United States
CitationJournal: Nature / Year: 2021
Title: Structural basis for ligand reception by anaplastic lymphoma kinase.
Authors: Li, T. / Stayrook, S.E. / Tsutsui, Y. / Zhang, J. / Wang, Y. / Li, H. / Proffitt, A. / Krimmer, S.G. / Ahmed, M. / Belliveau, O. / Walker, I.X. / Mudumbi, K.C. / Suzuki, Y. / Lax, I. / ...Authors: Li, T. / Stayrook, S.E. / Tsutsui, Y. / Zhang, J. / Wang, Y. / Li, H. / Proffitt, A. / Krimmer, S.G. / Ahmed, M. / Belliveau, O. / Walker, I.X. / Mudumbi, K.C. / Suzuki, Y. / Lax, I. / Alvarado, D. / Lemmon, M.A. / Schlessinger, J. / Klein, D.E.
History
DepositionFeb 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 15, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ALK tyrosine kinase receptor


Theoretical massNumber of molelcules
Total (without water)31,8461
Polymers31,8461
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.141, 76.141, 230.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1029-

HOH

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Components

#1: Protein ALK tyrosine kinase receptor / Anaplastic lymphoma kinase


Mass: 31846.137 Da / Num. of mol.: 1 / Fragment: Glycine-rich domain residues 678-986
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALK / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9UM73, receptor protein-tyrosine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56 % / Description: plate
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Imidazole pH 8.0, 10% PEG 8000, 0.2 M Ca(OAc)2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 19, 2018 / Details: undulator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.91→43.43 Å / Num. obs: 30911 / % possible obs: 97.8 % / Redundancy: 15.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.036 / Rrim(I) all: 0.151 / Net I/σ(I): 13.1 / Num. measured all: 475077 / Scaling rejects: 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.91-1.9620.786280914080.6850.621.0080.769.3
8.98-43.4314.60.04959254070.9990.0130.05136.199.3

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Processing

Software
NameVersionClassification
PHENIXdev_3915refinement
XDS20200417data reduction
SCALA0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LIR

7lir


Resolution: 1.91→43.43 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2143 1518 4.93 %
Rwork0.188 29243 -
obs0.1893 30761 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.44 Å2 / Biso mean: 37.6674 Å2 / Biso min: 16.94 Å2
Refinement stepCycle: final / Resolution: 1.91→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 213 2411
Biso mean---43.36 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132246
X-RAY DIFFRACTIONf_angle_d1.2973035
X-RAY DIFFRACTIONf_dihedral_angle_d7.334320
X-RAY DIFFRACTIONf_chiral_restr0.081307
X-RAY DIFFRACTIONf_plane_restr0.011411
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.980.37891030.31141997210076
1.98-2.050.30071510.25662590274198
2.05-2.130.25541480.211226612809100
2.13-2.230.27531330.211226532786100
2.23-2.340.22121450.184826722817100
2.34-2.490.20681300.171226922822100
2.49-2.680.20641400.175827012841100
2.68-2.950.2541160.190827462862100
2.95-3.380.19971360.179427472883100
3.38-4.260.20051520.166527982950100
4.26-43.430.17661640.186829863150100

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