[English] 日本語
Yorodumi
- PDB-6at9: Crystal structure of an anaplastic lymphoma kinase-derived neurob... -

+
Open data


ID or keywords:

Loading...

-
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 / phosphorylation / positive regulation of dendrite development / regulation of neuron differentiation / peptidyl-tyrosine autophosphorylation / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / Signaling by ALK / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / adult behavior / endoplasmic reticulum exit site / response to stress / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 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 / detection of bacterium / negative regulation of lipid catabolic process / T cell receptor binding / energy homeostasis / transmembrane receptor protein tyrosine kinase activity / cell surface receptor protein tyrosine kinase signaling pathway / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / hippocampus development / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / positive regulation of NF-kappaB transcription factor activity / receptor protein-tyrosine kinase / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / Signaling by ALK fusions and activated point mutants / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / heparin binding
Similarity search - Function
: / ALK/LTK, Glycine-rich domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Low-density lipoprotein receptor domain class A / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / 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. / Low-density lipoprotein receptor domain class A / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / 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. / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Tyrosine-protein kinase, active site / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more