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- PDB-6at9: Crystal structure of an anaplastic lymphoma kinase-derived neurob... -

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Basic information

Entry
Database: PDB / ID: 6at9
TitleCrystal structure of an anaplastic lymphoma kinase-derived neuroblastoma tumor antigen bound to the Human Major Histocompatibility Complex Class I molecule HLA-A*0101
Components
  • ALK
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-1 alpha chain
KeywordsIMMUNE SYSTEM / lymphoma kinase-derived neuroblastoma tumor antigen / Human Major Histocompatibility Complex Class I / MHC-I / Complex
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 / regulation of neuron differentiation / positive regulation of dendrite development / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / Signaling by ALK / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / phosphorylation / CD8 receptor binding / response to stress / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / adult behavior / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / neuron development / negative regulation of lipid catabolic process / detection of bacterium / T cell receptor binding / peptidyl-tyrosine autophosphorylation / energy homeostasis / transmembrane receptor protein tyrosine kinase activity / : / : / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / hippocampus development / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / placental growth factor receptor activity / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / T cell mediated cytotoxicity / receptor protein-tyrosine kinase / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / positive regulation of type II interferon production / specific granule lumen / recycling endosome membrane
Similarity search - Function
: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily ...: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / : / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / ALK tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9503 Å
AuthorsToor, J. / Rao, A.A. / Salama, S. / Tripathi, S. / Haussler, D. / Sgourakis, N.G.
CitationJournal: Front Immunol / Year: 2018
Title: A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations.
Authors: Toor, J.S. / Rao, A.A. / McShan, A.C. / Yarmarkovich, M. / Nerli, S. / Yamaguchi, K. / Madejska, A.A. / Nguyen, S. / Tripathi, S. / Maris, J.M. / Salama, S.R. / Haussler, D. / Sgourakis, N.G.
History
DepositionAug 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: Beta-2-microglobulin
C: ALK


Theoretical massNumber of molelcules
Total (without water)45,6983
Polymers45,6983
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-15 kcal/mol
Surface area18510 Å2
Unit cell
Length a, b, c (Å)81.410, 81.410, 118.281
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein HLA class I histocompatibility antigen, A-1 alpha chain / MHC class I antigen A*1


Mass: 32567.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30443, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61769
#3: Protein/peptide ALK


Mass: 1250.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UM73*PLUS
Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.18M MgCl2, 0.1M Na-HEPES(7.5),27%PEG400, 10%Glycerol
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 2.95→45.31 Å / Num. obs: 9982 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.2
Reflection shellResolution: 2.95→3.13 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3 / Num. unique obs: 1590 / CC1/2: 0.876 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W72

1w72


Resolution: 2.9503→45.31 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.06
RfactorNum. reflection% reflection
Rfree0.3073 1014 10.18 %
Rwork0.2241 --
obs0.2324 9956 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9503→45.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3153 0 0 0 3153
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033241
X-RAY DIFFRACTIONf_angle_d0.724394
X-RAY DIFFRACTIONf_dihedral_angle_d6.9481921
X-RAY DIFFRACTIONf_chiral_restr0.046442
X-RAY DIFFRACTIONf_plane_restr0.004581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9503-3.10580.43541390.28881245X-RAY DIFFRACTION99
3.1058-3.30040.36061420.28631246X-RAY DIFFRACTION99
3.3004-3.55510.32471430.25471262X-RAY DIFFRACTION100
3.5551-3.91270.34031400.23471268X-RAY DIFFRACTION100
3.9127-4.47840.33631440.20791270X-RAY DIFFRACTION100
4.4784-5.64060.26971500.19611286X-RAY DIFFRACTION100
5.6406-45.31550.26311560.21161365X-RAY DIFFRACTION100
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)
11.09560.03150.03030.27430.18910.3889-0.22330.20880.62460.6511-0.0926-0.1214-0.50970.1651-0.16250.7209-0.025-0.13280.2550.06580.435767.851456.4837130.4896
20.0912-0.03740.02610.1005-0.0480.1527-0.2639-0.0480.010.2227-0.0426-0.2899-0.33270.0315-0.06910.402-0.05170.07120.52760.18920.679965.172351.7724118.5624
30.0618-0.081-0.13820.13360.13450.1779-0.02090.2225-0.0284-0.2827-0.0958-0.061-0.1948-0.0227-0.03350.3259-0.0559-0.09880.3980.16260.419663.406557.2068110.467
40.2848-0.03130.1694-0.00110.02760.96220.03680.34580.36930.1381-0.5468-0.57290.32450.6559-0.64620.0355-0.1256-0.3570.47380.18760.794882.318432.4591127.7026
50.1012-0.05210.03710.1022-0.0250.07010.25730.1485-0.19710.1038-0.4145-0.17340.04040.19730.00130.38310.0663-0.16750.46620.03040.642280.666421.4464124.7278
60.18470.09270.19160.14230.03390.23820.18260.0918-0.12620.3415-0.041-0.29020.1133-0.11970.06970.5185-0.1779-0.22460.47310.30460.128268.868531.9336135.9429
70.11-0.09050.05640.0987-0.08490.04270.2265-0.0405-0.09320.4014-0.0061-0.26020.20740.08260.02330.7386-0.1135-0.08150.53910.04120.321664.633536.4589141.6499
80.04810.0355-0.00720.05960.00680.0242-0.02450.0670.107-0.02120.03940.0686-0.03030.0298-0.00240.5294-0.05970.06350.28030.00450.333965.633344.1854125.6526
90.8023-0.079-0.32990.0902-0.1390.48310.16660.08020.21810.1843-0.08150.00070.1444-0.14820.21530.9938-0.0139-0.57810.18060.2614-0.189670.314232.5567143.8223
100.03670.10250.05840.23090.10820.0490.13840.1716-0.06720.4368-0.0185-0.12010.0533-0.26610.12640.65570.05370.0780.48110.21620.281856.279232.2075138.1257
110.1067-0.03160.09890.3805-0.03530.1420.21320.1264-0.06490.40160.3771-0.21480.2448-0.07640.06010.9074-0.0383-0.13220.5050.06870.396668.06324.0076139.6947
120.07840.01640.01940.52170.49070.4772-0.0702-0.03920.07150.36720.2892-0.3598-0.14840.05210.05690.79840.01810.05160.72520.25610.483164.970363.0126120.0258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 274 )
6X-RAY DIFFRACTION6chain 'B' and (resid 0 through 19 )
7X-RAY DIFFRACTION7chain 'B' and (resid 20 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 61 )
9X-RAY DIFFRACTION9chain 'B' and (resid 62 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 90 )
11X-RAY DIFFRACTION11chain 'B' and (resid 91 through 99 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 10 )

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