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- PDB-7nwz: ALK:ALKAL2 complex -

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Basic information

Entry
Database: PDB / ID: 7nwz
TitleALK:ALKAL2 complex
Components
  • ALK and LTK ligand 2
  • ALK tyrosine kinase receptor
KeywordsPROTEIN BINDING / Cell Surface Receptor Cytokine binding Cytokine receptor complex
Function / homology
Function and homology information


positive regulation of ERK5 cascade / 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 ...positive regulation of ERK5 cascade / 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 / transmembrane receptor protein tyrosine kinase activator activity / 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 / cytokine activity / hippocampus development / receptor protein-tyrosine kinase / receptor tyrosine kinase binding / positive regulation of neuron projection development / 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 / positive regulation of ERK1 and ERK2 cascade / receptor complex / phosphorylation / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
ALK and LTK ligand 1/2 / ALK and LTK ligand 1/2 / 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 ...ALK and LTK ligand 1/2 / ALK and LTK ligand 1/2 / 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 and LTK ligand 2 / ALK tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.17 Å
AuthorsDe Munck, S. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Nature / Year: 2021
Title: Structural basis of cytokine-mediated activation of ALK family receptors.
Authors: De Munck, S. / Provost, M. / Kurikawa, M. / Omori, I. / Mukohyama, J. / Felix, J. / Bloch, Y. / Abdel-Wahab, O. / Bazan, J.F. / Yoshimi, A. / Savvides, S.N.
History
DepositionMar 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 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 1.2Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
D: ALK and LTK ligand 2
F: ALK tyrosine kinase receptor
E: ALK tyrosine kinase receptor
B: ALK tyrosine kinase receptor
A: ALK tyrosine kinase receptor
C: ALK and LTK ligand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,87512
Polymers161,5476
Non-polymers1,3276
Water00
1
D: ALK and LTK ligand 2
F: ALK tyrosine kinase receptor
E: ALK tyrosine kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,2165
Polymers80,7743
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-12 kcal/mol
Surface area26900 Å2
MethodPISA
2
B: ALK tyrosine kinase receptor
A: ALK tyrosine kinase receptor
C: ALK and LTK ligand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6587
Polymers80,7743
Non-polymers8854
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-11 kcal/mol
Surface area26690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.910, 97.910, 356.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
13
23
33

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 684 through 706 or resid 708...A684 - 706
121(chain 'A' and (resid 684 through 706 or resid 708...A708 - 716
131(chain 'A' and (resid 684 through 706 or resid 708...A718 - 751
141(chain 'A' and (resid 684 through 706 or resid 708...A753 - 855
151(chain 'A' and (resid 684 through 706 or resid 708...A857 - 981
161(chain 'A' and (resid 684 through 706 or resid 708...A983
271(chain 'B' and (resid 684 through 706 or resid 708...B684 - 706
281(chain 'B' and (resid 684 through 706 or resid 708...B708 - 716
291(chain 'B' and (resid 684 through 706 or resid 708...B718 - 751
2101(chain 'B' and (resid 684 through 706 or resid 708...B753 - 855
2111(chain 'B' and (resid 684 through 706 or resid 708...B857 - 981
2121(chain 'B' and (resid 684 through 706 or resid 708...B983
3131(chain 'E' and (resid 684 through 706 or resid 708...E684 - 706
3141(chain 'E' and (resid 684 through 706 or resid 708...E708 - 716
3151(chain 'E' and (resid 684 through 706 or resid 708...E718 - 751
3161(chain 'E' and (resid 684 through 706 or resid 708...E753 - 855
3171(chain 'E' and (resid 684 through 706 or resid 708...E857 - 981
3181(chain 'E' and (resid 684 through 706 or resid 708...E983
4191(chain 'F' and (resid 684 through 706 or resid 708...F684 - 706
4201(chain 'F' and (resid 684 through 706 or resid 708...F708 - 716
4211(chain 'F' and (resid 684 through 706 or resid 708...F718 - 751
4221(chain 'F' and (resid 684 through 706 or resid 708...F753 - 855
4231(chain 'F' and (resid 684 through 706 or resid 708...F857 - 981
4241(chain 'F' and (resid 684 through 706 or resid 708...F983
1252(chain 'C' and resid 93 through 149)C93 - 149
2262(chain 'D' and resid 93 through 149)D93 - 149
1273chain 'G'G1
2283chain 'H'H1
3293chain 'J'J1

NCS ensembles :
ID
1
2
3

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Components

#1: Protein ALK and LTK ligand 2 / Augmentor alpha / AUG-alpha / Protein FAM150B


Mass: 9567.136 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALKAL2, FAM150B, UNQ542/PRO1097 / Production host: Homo sapiens (human) / References: UniProt: Q6UX46
#2: Protein
ALK tyrosine kinase receptor / Anaplastic lymphoma kinase


Mass: 35603.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALK / Production host: Homo sapiens (human)
References: UniProt: Q9UM73, receptor protein-tyrosine kinase
#3: 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.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
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 interestN

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / Details: 0.1M MES pH 6.5 15% w/v PEG 6000 5% w/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 4.17→48.96 Å / Num. obs: 13681 / % possible obs: 93.8 % / Redundancy: 25.7 % / Biso Wilson estimate: 101.52 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.206 / Net I/σ(I): 13.9
Reflection shellResolution: 4.17→4.32 Å / Num. unique obs: 942 / CC1/2: 0.89 / Rrim(I) all: 1.68

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7NX4

7nx4


Resolution: 4.17→48.96 Å / SU ML: 0.5339 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2676 897 6.95 %
Rwork0.2552 12006 -
obs0.2561 12903 93.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 163.33 Å2
Refinement stepCycle: LAST / Resolution: 4.17→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9754 0 84 0 9838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002210062
X-RAY DIFFRACTIONf_angle_d0.482213608
X-RAY DIFFRACTIONf_chiral_restr0.04521410
X-RAY DIFFRACTIONf_plane_restr0.0031818
X-RAY DIFFRACTIONf_dihedral_angle_d14.90373538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.17-4.430.31481110.29781571X-RAY DIFFRACTION75.43
4.43-4.770.27781370.28291842X-RAY DIFFRACTION88.9
4.77-5.250.29771550.27222045X-RAY DIFFRACTION98.48
5.25-6.010.31091600.27612108X-RAY DIFFRACTION99.96
6.01-7.570.27631620.26422158X-RAY DIFFRACTION100
7.57-48.960.21951720.21472282X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.060386901971.033233724060.4638616865911.002943301630.4518878813430.202982575769-0.0614371150969-0.469024072028-0.2169301637510.374609345090.6166286806140.9972846298360.111071195526-1.38854916908-0.4212787126421.16161460718-0.4346336562730.007268212124983.35200997510.6561018591191.4993255184811.7379132552-22.59203928332.8561369695
21.8877141547-1.62082664072-0.2865551893524.04168156851.646103021792.056986542390.290181382949-0.51317061543-0.600318395892-1.17711448340.1004178658050.549862286839-0.403979489176-0.667277079626-0.3818409028931.17682258796-0.569697901635-0.1090886024091.581851479320.2745400062111.1222252849731.0770155753-18.031254151312.2351968684
30.892710124036-0.00388505415817-1.141357508462.331309922941.144873821292.91386588553-0.595908811738-0.096588144483-1.4378045353-1.06079888460.72723880347-0.123551087221-0.1262174434-0.9179472214070.01769851714541.53079398514-0.952388084513-0.2068099827912.243133910050.349432382262.5766082432711.707557739-39.545812186315.4809399024
42.020125674770.797208101486-0.4552560923262.157619942510.02488245866131.01581597662-0.03831839648020.554877585617-0.0319916749373-0.2110153570320.2669320623660.06618820650580.4598595953540.232308242786-0.1939270263831.146231113940.9475895372360.1326234591451.474129918680.09545153314291.1044935717918.5831533878-6.9542396386566.2347154109
52.031509997760.75727460315-0.8709939555833.202567381771.61548807232.53715342161-0.4925771242360.6085713146550.29698468047-0.6423344273420.762344999650.322643565779-0.911916552357-0.183156121818-0.2529858146041.300602520230.400090328924-0.02990655544171.656048473480.274991174381.0774945891317.547894929610.847046312743.7085097314
60.7620374415930.0973453513551-0.6821105815842.099237425380.117434687332.292407770290.4941316494010.2577200185510.702201308210.1267174921090.4510493588110.52675264991-0.995878847698-0.0637229481147-0.8466460585631.898495507020.6967437913580.2020904138491.268507544380.03263883235061.4949548846818.268690192321.483664225865.3682542965
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D92 - 149
2X-RAY DIFFRACTION2F679 - 985
3X-RAY DIFFRACTION3E679 - 985
4X-RAY DIFFRACTION4B678 - 986
5X-RAY DIFFRACTION5A678 - 986
6X-RAY DIFFRACTION6C92 - 149

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