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- PDB-7mj9: HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide -

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Basic information

Entry
Database: PDB / ID: 7mj9
TitleHLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Insulin-like growth factor-binding protein-like 1 altered peptide
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / LYMPHOMA KINASE-DERIVED NEUROBLASTOMA TUMOR ANTIGEN / HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / COMPLEX
Function / homology
Function and homology information


cellular response to tumor cell / insulin-like growth factor binding / antigen processing and presentation / regulation of signal transduction / 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 ...cellular response to tumor cell / insulin-like growth factor binding / antigen processing and presentation / regulation of signal transduction / 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 / regulation of cell growth / 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 / 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 / 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 / early endosome membrane / protein refolding / protein homotetramerization / collagen-containing extracellular matrix / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / 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
Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. ...Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25 / Insulin-like growth factor binding protein / Insulin-like growth factor-binding protein, IGFBP / Insulin-like growth factor-binding protein (IGFBP) N-terminal domain profile. / Insulin growth factor-binding protein homologues / Kazal-type serine protease inhibitor domain / Kazal type serine protease inhibitors / Kazal domain superfamily / Kazal domain / Kazal domain profile. / Immunoglobulin I-set / Immunoglobulin I-set domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Growth factor receptor cysteine-rich domain superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 subtype / Immunoglobulin / 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / MHC class I antigen / Insulin-like growth factor-binding protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsToor, J.S. / Tripathi, S.M. / Truong, H.V. / Yarmarkovich, M. / Maris, J.M. / Sgourakis, N.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI143997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM125034 United States
CitationJournal: Nature / Year: 2021
Title: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs.
Authors: Yarmarkovich, M. / Marshall, Q.F. / Warrington, J.M. / Premaratne, R. / Farrel, A. / Groff, D. / Li, W. / di Marco, M. / Runbeck, E. / Truong, H. / Toor, J.S. / Tripathi, S. / Nguyen, S. / ...Authors: Yarmarkovich, M. / Marshall, Q.F. / Warrington, J.M. / Premaratne, R. / Farrel, A. / Groff, D. / Li, W. / di Marco, M. / Runbeck, E. / Truong, H. / Toor, J.S. / Tripathi, S. / Nguyen, S. / Shen, H. / Noel, T. / Church, N.L. / Weiner, A. / Kendsersky, N. / Martinez, D. / Weisberg, R. / Christie, M. / Eisenlohr, L. / Bosse, K.R. / Dimitrov, D.S. / Stevanovic, S. / Sgourakis, N.G. / Kiefel, B.R. / Maris, J.M.
History
DepositionApr 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 1, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
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

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Insulin-like growth factor-binding protein-like 1 altered peptide


Theoretical massNumber of molelcules
Total (without water)44,9943
Polymers44,9943
Non-polymers00
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-50 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.940, 80.130, 57.740
Angle α, β, γ (deg.)90.00, 114.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MHC class I antigen


Mass: 32082.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A*02:01 / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Insulin-like growth factor-binding protein-like 1 altered peptide / IGFBP-related protein 10 / Insulin-like growth factor-binding-related protein 4 / IGFBP-rP4


Mass: 1032.342 Da / Num. of mol.: 1 / Fragment: Residues 14-22 / Mutation: Residue 18 mutated to arginine / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WX77
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium Chloride, 0.1 M HEPES pH 7, 20 % PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03316 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.75→52.63 Å / Num. obs: 44403 / % possible obs: 98.4 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.8
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2298 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C07

5c07


Resolution: 1.75→52.63 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1944 2350 5.3 %
Rwork0.1604 --
obs0.1622 44313 98.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→52.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 10 329 3494
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113253
X-RAY DIFFRACTIONf_angle_d1.124415
X-RAY DIFFRACTIONf_dihedral_angle_d12.6591913
X-RAY DIFFRACTIONf_chiral_restr0.058450
X-RAY DIFFRACTIONf_plane_restr0.007574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78580.25871270.23952329X-RAY DIFFRACTION92
1.7858-1.82460.25071320.21452380X-RAY DIFFRACTION95
1.8246-1.8670.25981390.19622448X-RAY DIFFRACTION97
1.867-1.91370.2281220.18362445X-RAY DIFFRACTION98
1.9137-1.96550.21641320.17612449X-RAY DIFFRACTION97
1.9655-2.02330.21691260.16672467X-RAY DIFFRACTION98
2.0233-2.08860.21221450.16942452X-RAY DIFFRACTION98
2.0886-2.16330.17821420.15682485X-RAY DIFFRACTION98
2.1633-2.24990.21391500.1622457X-RAY DIFFRACTION98
2.2499-2.35230.21431430.16552474X-RAY DIFFRACTION99
2.3523-2.47630.18981410.16052459X-RAY DIFFRACTION99
2.4763-2.63140.21991340.16652495X-RAY DIFFRACTION99
2.6314-2.83460.22751650.17732485X-RAY DIFFRACTION99
2.8346-3.11980.20911620.16892484X-RAY DIFFRACTION99
3.1198-3.57120.17611100.15752551X-RAY DIFFRACTION99
3.5712-4.49890.14751550.13092511X-RAY DIFFRACTION100
4.4989-52.630.1751250.15042592X-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)
11.41750.5870.04993.0501-0.29971.6498-0.05970.1021-0.0588-0.25720.01870.04670.0414-0.0563-0.00860.1315-0.0172-0.01520.1583-0.00110.128178.0051-71.463756.408
21.85841.17961.57923.81212.03733.5311-0.11430.03270.1359-0.29740.05140.2757-0.2331-0.22450.14520.18780.0182-0.00560.20820.04620.190573.2847-61.663660.5257
32.12492.04410.27834.50720.59361.57840.0334-0.1258-0.11730.1796-0.0684-0.05280.0163-0.0999-0.01240.1103-0.0076-0.00550.15910.01520.129879.1652-69.150670.2811
41.7230.54170.70792.66831.04252.0870.0319-0.29460.11490.3809-0.16240.33590.1189-0.31350.07660.2179-0.01130.03980.2595-0.00460.187774.0947-64.534477.9786
53.1916-1.06870.81551.41090.00971.62540.45130.2556-0.5691-0.265-0.21020.26320.26820.1259-0.12630.26-0.0529-0.05060.15660.04280.180988.0037-91.420461.5824
64.7456-1.66152.78051.0972-1.01972.570.2255-0.4088-0.5111-0.03970.10060.13710.2955-0.0827-0.2470.2374-0.016-0.03620.24460.04190.232598.2783-95.60167.9776
73.57940.85370.52043.96924.16544.59960.0611-0.53470.41110.02870.0946-0.0605-0.23570.03010.0410.2523-0.02010.01820.314-0.01930.31898.7696-72.965562.6321
81.0087-2.2575-2.07658.25697.15796.2012-0.00790.2169-0.11850.1533-0.33020.18690.3615-0.52670.41130.2243-0.03650.01720.2435-0.02360.218196.6081-84.823150.7095
94.135-2.5521-3.29112.62723.24374.65580.33770.32080.3302-0.58730.014-0.37-0.71960.0681-0.42120.3299-0.02420.07440.23580.06380.281298.5915-71.545648.9049
103.1355-2.4998-3.58174.87295.09016.8883-0.0630.0165-0.05240.0381-0.0182-0.01860.20470.07190.1780.1922-0.008-0.00920.16750.02450.198890.7356-75.170857.5794
111.74631.15530.31511.57260.57132.3360.042-0.01680.2427-0.3190.4819-0.836-0.26940.768-0.35080.2165-0.08760.06010.3406-0.05230.4031105.8185-74.889751.3287
128.58320.74261.56872.00533.46476.90580.1804-0.42550.04880.5779-0.0438-0.77840.6420.4515-0.1580.28730.0033-0.00460.343-0.00720.2657106.5541-83.912153.6245
132.04441.21041.34251.97231.81271.64970.0612-0.05110.1862-0.0791-0.19980.5479-0.1562-0.49350.29130.2186-0.00240.02990.28820.03080.290969.3475-64.331666.1703
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 163 )
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 207 )
6X-RAY DIFFRACTION6chain 'A' and (resid 208 through 276 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 12 )
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 72 )
11X-RAY DIFFRACTION11chain 'B' and (resid 73 through 91 )
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 9 )

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