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- PDB-7mj6: HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide -

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Basic information

Entry
Database: PDB / ID: 7mj6
TitleHLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
Components
  • Beta-2-microglobulin
  • Insulin-like growth factor-binding protein-like 1 peptide
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / NEUROBLASTOMA TUMOR ANTIGEN / IGFBPL1 / 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 of peptide antigen via MHC class I / regulation of signal transduction / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding ...cellular response to tumor cell / insulin-like growth factor binding / antigen processing and presentation of peptide antigen via MHC class I / regulation of signal transduction / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / regulation of cell growth / 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 / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / positive regulation of T cell activation / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / positive regulation of protein binding / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / ER-Phagosome pathway / early endosome membrane / protein refolding / collagen-containing extracellular matrix / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / lysosomal membrane / external side of plasma 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 / identical protein binding / membrane / metal ion 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 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: 1.95 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2266
Polymers44,9503
Non-polymers2763
Water4,558253
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-24 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.410, 78.980, 60.370
Angle α, β, γ (deg.)90.00, 97.43, 90.00
Int Tables number5
Space group name H-MC121

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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


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 (E. coli) / References: UniProt: P61769
#3: Protein/peptide Insulin-like growth factor-binding protein-like 1 peptide / IGFBP-related protein 10 / Insulin-like growth factor-binding-related protein 4 / IGFBP-rP4


Mass: 988.306 Da / Num. of mol.: 1 / Fragment: Residues 14-22 / Source method: obtained synthetically / Details: Neuroblastoma-Derived / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WX77
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.93 Å3/Da / Density % sol: 58.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 1M Sodium Citrate Dibasic, 0.1M Sodium Cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11584 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11584 Å / Relative weight: 1
ReflectionResolution: 1.95→64.25 Å / Num. obs: 37547 / % possible obs: 99.2 % / Redundancy: 6.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.135 / Net I/σ(I): 9
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2616 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C07

5c07


Resolution: 1.95→64.25 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 1929 5.14 %
Rwork0.1576 --
obs0.1596 37531 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→64.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 18 253 3415
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073372
X-RAY DIFFRACTIONf_angle_d0.7854593
X-RAY DIFFRACTIONf_dihedral_angle_d17.3652007
X-RAY DIFFRACTIONf_chiral_restr0.052470
X-RAY DIFFRACTIONf_plane_restr0.006602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99880.24461430.21812504X-RAY DIFFRACTION99
1.9988-2.05280.21471460.19982529X-RAY DIFFRACTION99
2.0528-2.11320.22411240.19132523X-RAY DIFFRACTION99
2.1132-2.18140.2111540.1822525X-RAY DIFFRACTION99
2.1814-2.25940.22651490.18172524X-RAY DIFFRACTION99
2.2594-2.34990.23641380.17652538X-RAY DIFFRACTION99
2.3499-2.45680.22341190.17432554X-RAY DIFFRACTION99
2.4568-2.58640.20271420.16492515X-RAY DIFFRACTION99
2.5864-2.74840.20231500.16152526X-RAY DIFFRACTION99
2.7484-2.96060.21261270.15792558X-RAY DIFFRACTION99
2.9606-3.25850.21121200.14792580X-RAY DIFFRACTION100
3.2585-3.730.17411330.13892556X-RAY DIFFRACTION99
3.73-4.69920.14811570.12172540X-RAY DIFFRACTION99
4.6992-64.250.20091270.15992630X-RAY DIFFRACTION99
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)
11.3379-0.0530.03911.91330.03921.51540.07640.1131-0.0293-0.2903-0.0234-0.0140.04040.0392-0.05220.19740.0136-0.010.12730.0170.1105114.129-61.293119.435
22.20470.7244-0.00012.63170.70871.8720.0773-0.1713-0.1540.0256-0.02610.04370.069-0.1074-0.0320.17690.0037-0.0430.13690.01330.1427108.479-63.321130.853
31.5652-0.47160.37252.58410.95931.69210.1093-0.1621-0.07560.0288-0.20480.40.1328-0.33330.10160.2082-0.04440.00230.21140.01960.174100.866-62.671129.98
43.0074-1.37772.26381.9256-1.92134.41390.2641-0.0782-0.1611-0.1892-0.17510.04840.52040.4185-0.01490.29720.06790.02060.23850.02020.1516127.007-88.884131.993
51.277-0.56921.53011.7753-1.86455.03170.0198-0.2558-0.02320.107-0.0818-0.0412-0.03980.03160.01550.18260.0186-0.00090.19630.01540.1353126.914-85.894140.293
62.5513-0.21813.01191.9541-1.42776.45270.4744-0.0557-0.4091-0.17640.02970.07280.94940.0696-0.33130.3140.0161-0.01720.2480.04310.1904126.217-95.731141.651
72.7829-3.1261-4.67453.97045.21297.8676-0.0159-0.1980.61990.1672-0.03990.3455-0.5558-0.63350.08060.40850.0895-0.15480.4782-0.1420.4065125.191-58.587139.818
83.71640.35110.81761.99762.64134.4112-0.2211-0.2340.0518-0.02910.1737-0.2616-0.1265-0.23420.03160.28140.0207-0.05080.18720.01450.1758132.855-74.458132.84
92.6699-2.2321-1.75394.51172.41742.39550.0310.1078-0.0972-0.0415-0.164-0.06570.0921-0.11840.13430.2246-0.0003-0.03560.1765-0.01110.2084134.546-77.865126.076
106.8844-6.6749-5.50456.83264.8644.94210.37210.24540.9749-0.3835-0.0004-0.9311-0.4843-0.0285-0.35750.2171-0.00470.03460.2365-0.02290.3801133.984-62.6129.091
113.8144-2.60233.87454.2068-1.9655.7354-0.11721.3991.0869-0.3911-0.052-0.6548-0.61030.67980.09780.3087-0.05610.07150.30050.06480.4773140.422-67.088121.053
126.7139-4.8165-2.40674.32882.32211.6389-0.3044-0.0028-0.35040.2172-0.00790.10790.16160.02730.33730.192-0.0089-0.00430.1370.00850.182125.647-68.731127.566
139.6752-0.83851.20652.34752.0972.28030.3343-0.362-0.28650.65820.427-1.08470.38181.2614-0.60820.35650.0503-0.03690.4754-0.07390.6947149.314-79.696126.643
140.17550.12930.2532.09610.5480.4656-0.0764-0.49140.7615-0.14730.5469-1.1298-0.36960.4925-0.42930.2641-0.0067-0.08420.274-0.15130.5203137.842-62.421134.215
156.20330.8347-0.57981.97-0.16296.0637-0.1244-0.8161-0.1480.5108-0.1614-0.32160.49810.38760.27280.25880.078-0.06550.3154-0.00280.331140.417-76.472134.226
164.17341.0541.69256.80220.50053.65360.1205-0.14570.1652-0.3319-0.29860.57620.2097-0.170.12620.1723-0.01840.00230.23130.0070.1952103.496-58.738121.707
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:84 )A2 - 84
2X-RAY DIFFRACTION2( CHAIN A AND RESID 85:118 )A85 - 118
3X-RAY DIFFRACTION3( CHAIN A AND RESID 119:174 )A119 - 174
4X-RAY DIFFRACTION4( CHAIN A AND RESID 175:197 )A175 - 197
5X-RAY DIFFRACTION5( CHAIN A AND RESID 198:250 )A198 - 250
6X-RAY DIFFRACTION6( CHAIN A AND RESID 251:276 )A251 - 276
7X-RAY DIFFRACTION7( CHAIN B AND RESID 2:6 )B2 - 6
8X-RAY DIFFRACTION8( CHAIN B AND RESID 7:12 )B7 - 12
9X-RAY DIFFRACTION9( CHAIN B AND RESID 13:31 )B13 - 31
10X-RAY DIFFRACTION10( CHAIN B AND RESID 32:42 )B32 - 42
11X-RAY DIFFRACTION11( CHAIN B AND RESID 43:52 )B43 - 52
12X-RAY DIFFRACTION12( CHAIN B AND RESID 53:72 )B53 - 72
13X-RAY DIFFRACTION13( CHAIN B AND RESID 73:78 )B73 - 78
14X-RAY DIFFRACTION14( CHAIN B AND RESID 79:91 )B79 - 91
15X-RAY DIFFRACTION15( CHAIN B AND RESID 92:100 )B92 - 100
16X-RAY DIFFRACTION16( CHAIN C AND RESID 1:9 )C1 - 9

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