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- PDB-5txs: Crystal structure of an anaplastic lymphoma kinase-derived neurob... -

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Basic information

Entry
Database: PDB / ID: 5txs
TitleCrystal structure of an anaplastic lymphoma kinase-derived neuroblastoma tumor antigen bound to the Human Major Histocompatibility Complex Class I molecule HLA-B*1501
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-15 alpha chain
  • anapestic lymphoma kinase-derived neuroblastoma tumor antigen
KeywordsIMMUNE SYSTEM / lymphoma kinase-derived neuroblastoma tumor antigen / Human Major Histocompatibility Complex Class I / MHC-I / Complex
Function / homology
Function and homology information


regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / defense response / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
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 ...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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.697 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
DepositionNov 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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

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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, B-15 alpha chain
B: Beta-2-microglobulin
C: anapestic lymphoma kinase-derived neuroblastoma tumor antigen


Theoretical massNumber of molelcules
Total (without water)47,4753
Polymers47,4753
Non-polymers00
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-16 kcal/mol
Surface area18760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.442, 82.186, 109.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-15 alpha chain / MHC class I antigen B*15


Mass: 34508.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30464, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / 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 anapestic lymphoma kinase-derived neuroblastoma tumor antigen


Mass: 1087.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.4 Å3/Da / Density % sol: 48.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (6.5) 20% PEG 6000 / PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 51234 / % possible obs: 99.93 % / Redundancy: 8.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Net I/σ(I): 11.22
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 1.83 / CC1/2: 0.812 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XR8

1xr8


Resolution: 1.697→45.84 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.16
RfactorNum. reflection% reflection
Rfree0.1964 2000 3.9 %
Rwork0.1554 --
obs0.157 51234 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.697→45.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3167 0 0 544 3711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123371
X-RAY DIFFRACTIONf_angle_d1.344594
X-RAY DIFFRACTIONf_dihedral_angle_d13.8681260
X-RAY DIFFRACTIONf_chiral_restr0.057464
X-RAY DIFFRACTIONf_plane_restr0.007615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6975-1.73990.26851400.21273448X-RAY DIFFRACTION99
1.7399-1.7870.27051410.20533459X-RAY DIFFRACTION100
1.787-1.83950.25281390.18743440X-RAY DIFFRACTION100
1.8395-1.89890.22681420.17743495X-RAY DIFFRACTION100
1.8989-1.96680.20581420.17373484X-RAY DIFFRACTION100
1.9668-2.04550.20471410.15483472X-RAY DIFFRACTION100
2.0455-2.13860.20861410.15433474X-RAY DIFFRACTION100
2.1386-2.25140.18261420.1553509X-RAY DIFFRACTION100
2.2514-2.39240.19431440.15183524X-RAY DIFFRACTION100
2.3924-2.57710.20941420.15573499X-RAY DIFFRACTION100
2.5771-2.83640.2151450.16413550X-RAY DIFFRACTION100
2.8364-3.24680.20981430.15733537X-RAY DIFFRACTION100
3.2468-4.09020.16431450.14293581X-RAY DIFFRACTION100
4.0902-45.85660.16951530.13663762X-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)
10.15060.0531-0.13910.00650.13540.13880.0215-0.0655-0.1046-0.0345-0.0049-0.06840.03750.03490.00420.1305-0.0009-0.01980.120.0320.179610.15595.6388140.2375
20.27610.0626-0.02160.12250.07440.25540.01440.0226-0.11610.1673-0.1830.3060.01260.0136-0.67310.0982-0.03090.00820.0660.094-0.0719-0.516.7669145.5805
30.1963-0.22490.00850.17520.0050.07570.0054-0.03780.0325-0.0521-0.0037-0.0414-0.0371-0.009200.1253-0.0065-0.00260.1001-0.00670.1286-0.197617.8754135.1362
40.00630.0119-0.00050.0486-0.00770.0063-0.0665-0.17530.1583-0.0111-0.00470.0556-0.0728-0.0916-00.15350.01670.00550.1726-0.03140.1748-4.901422.2695143.5383
50.139-0.02210.10130.1263-0.05510.0581-0.0531-0.0489-0.0468-0.014-0.01160.0038-0.0280.144200.1403-0.0126-0.00280.17-0.02880.139924.306615.1095129.3187
60.1272-0.1807-0.1390.0872-0.0620.27990.04180.0164-0.01720.0029-0.0158-0.0003-0.18540.00950.02090.1779-0.00570.01670.1479-0.00010.098625.052616.5473111.9839
70.00510.0208-0.00230.0549-0.01040.0379-0.02640.0176-0.0357-0.1460.0264-0.08850.0706-0.1046-00.1593-0.01170.02710.19-0.02750.15297.6463.8526118.9902
80.0221-0.02210.00560.01440.0010.02780.0059-0.0854-0.014-0.0290.0867-0.0884-0.03690.05970.01940.12160.04080.0890.2797-0.18540.53132.1934-2.4938119.6747
90.00480.0050.01630.0167-0.020.08460.0577-0.0275-0.124-0.05380.1082-0.2427-0.0350.09870.0160.13470.01690.01860.1668-0.02460.258817.8298-0.1639122.5661
100.01680.0070.04150.0171-0.02320.1241-0.06060.0084-0.1934-0.0260.0696-0.2086-0.0206-0.099-0.01660.1489-0.01880.05590.1647-0.0140.25268.5086-5.1039122.7491
11-0.00060.0022-0.00390.00690.0034-0.0027-0.0772-0.107-0.2481-0.0193-0.0077-0.21390.1204-0.0464-00.27570.01410.02470.21420.07880.50317.2969-12.1972124.1966
120.0880.06840.10560.0280.05650.14110.0851-0.2757-0.08330.0323-0.052-0.1785-0.11440.0462-0.02260.1243-0.00510.01140.16370.04960.167213.10392.6148127.3521
130.0032-0.01720.02270.0287-0.02780.2385-0.07530.1293-0.2973-0.31430.1125-0.19690.1462-0.14620.0610.2152-0.01390.08680.1888-0.11090.344413.7243-7.5138114.9205
140.0481-0.0473-0.02250.072-0.01450.0730.0550.0666-0.035-0.07570.0494-0.0353-0.07730.01310.0880.2444-0.04970.10690.2821-0.1260.279819.8933-2.0519111.6824
150.0017-0.00690.005-0.01230.00690.0030.0157-0.08410.01640.1092-0.06440.04750.0678-0.019100.1217-0.01890.01730.1638-0.01480.1322-1.015813.7401146.4263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 137 )
4X-RAY DIFFRACTION4chain 'A' and (resid 138 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 197 )
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 11 )
8X-RAY DIFFRACTION8chain 'B' and (resid 12 through 19 )
9X-RAY DIFFRACTION9chain 'B' and (resid 20 through 30 )
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 41 )
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 51 )
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 90 )
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 99 )
15X-RAY DIFFRACTION15chain 'C' and (resid 1 through 9 )

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