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- PDB-7mj8: HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide -

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Basic information

Entry
Database: PDB / ID: 7mj8
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 / 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 ...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 / 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 / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / regulation of cell growth / 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 / 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 / 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 / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / : / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / 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 / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / metal ion binding / identical protein binding / membrane / 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/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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: 1.79 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 23, 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

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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)45,3144
Polymers45,2213
Non-polymers921
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.700, 79.020, 60.240
Angle α, β, γ (deg.)90.00, 97.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

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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 / 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 peptide / IGFBP-related protein 10 / Insulin-like growth factor-binding-related protein 4 / IGFBP-rP4


Mass: 1259.577 Da / Num. of mol.: 1 / Fragment: Residues 14-25 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
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: 1.11583 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: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.79→64.34 Å / Num. obs: 48080 / % possible obs: 98.2 % / Redundancy: 5.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.079 / Net I/σ(I): 10.7
Reflection shellResolution: 1.79→1.83 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2814 / CC1/2: 0.88

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C07

5c07


Resolution: 1.79→59.773 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1895 2532 5.27 %
Rwork0.1542 --
obs0.1561 48064 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.79→59.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 6 276 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093278
X-RAY DIFFRACTIONf_angle_d1.0214451
X-RAY DIFFRACTIONf_dihedral_angle_d17.7781941
X-RAY DIFFRACTIONf_chiral_restr0.056455
X-RAY DIFFRACTIONf_plane_restr0.007579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.82440.31641320.25812495X-RAY DIFFRACTION97
1.8244-1.86170.27081290.22652557X-RAY DIFFRACTION99
1.8617-1.90220.27121560.20822521X-RAY DIFFRACTION99
1.9022-1.94640.21731480.18332541X-RAY DIFFRACTION98
1.9464-1.99510.19881250.16882510X-RAY DIFFRACTION98
1.9951-2.04910.20371390.16412491X-RAY DIFFRACTION98
2.0491-2.10930.20661230.15872523X-RAY DIFFRACTION97
2.1093-2.17740.19571290.15362510X-RAY DIFFRACTION97
2.1774-2.25530.17561540.15332518X-RAY DIFFRACTION99
2.2553-2.34560.18851500.16052521X-RAY DIFFRACTION99
2.3456-2.45230.20641420.15782545X-RAY DIFFRACTION98
2.4523-2.58160.20141480.16282512X-RAY DIFFRACTION98
2.5816-2.74340.17851450.16152476X-RAY DIFFRACTION96
2.7434-2.95520.17691240.16292579X-RAY DIFFRACTION99
2.9552-3.25250.1941470.15572551X-RAY DIFFRACTION99
3.2525-3.72310.18631550.14222535X-RAY DIFFRACTION98
3.7231-4.69050.1441300.11612543X-RAY DIFFRACTION97
4.6905-59.7730.19041560.1512604X-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)
11.2182-0.09570.09961.02330.15541.14490.0737-0.045-0.0187-0.1672-0.04280.025-0.0245-0.106900.1911-0.0046-0.00720.15080.00550.142213.642612.26495.7895
20.3710.1339-0.35780.76140.10610.67510.1999-0.1037-0.318-0.308-0.02840.16680.26590.1226-0.16070.2633-0.0205-0.02750.15960.00290.152325.6297-11.52119.4042
30.3972-0.05580.10630.2966-0.30370.42330.0419-0.18190.0052-0.03220.02840.02560.1021-0.04540.00110.1705-0.00550.0010.20590.03230.161130.2456-15.645420.7523
40.17330.148-0.08530.1054-0.07640.04880.0485-0.2908-0.0696-0.0130.0139-0.0809-0.0914-0.0575-0.00290.21130.0195-0.01980.2231-0.04660.177533.32737.080316.6805
50.20460.13780.00870.1219-0.03410.0618-0.01520.1816-0.080.0837-0.1306-0.09350.0876-0.2058-00.17440.00550.0210.193-0.02690.253639.0892-4.82276.2774
60.0808-0.06640.15310.0207-0.0730.3880.0260.11940.2286-0.1787-0.0429-0.2884-0.3828-0.0813-0.0110.2411-0.00730.06490.2225-0.00690.359538.26410.90029.4433
70.4597-0.235-0.23120.14840.18940.27660.1830.53340.338-0.2506-0.0119-0.1955-0.40330.19240.00470.2018-0.03450.13790.29020.05780.451944.9616.30311.5782
80.13420.0951-0.05650.33770.0345-0.0899-0.0942-0.0102-0.31220.0089-0.06440.05810.0251-0.0362-0.00010.22290.020.03180.18760.01060.204630.05714.77577.9679
90.00010.0050.00570.00820.01160.00740.29-0.0671-0.14630.24390.1476-0.1804-0.09090.225300.21730.0111-0.05280.3748-0.12490.606453.6604-6.35967.3529
100.0035-0.0025-0.00770.00840.0038-0.00830.0306-0.16290.4520.01510.0567-0.544-0.1970.18580.00020.241-0.0267-0.0250.2548-0.12120.441242.176210.961814.622
110.0315-0.00780.02790.0093-0.01140.0393-0.0252-0.4769-0.19270.21830.0308-0.26170.06260.1011-0.00010.26030.0404-0.0410.2937-0.01520.361144.7225-3.068114.7132
120.02450.00080.02110.0141-0.02210.05920.06150.0593-0.0722-0.31920.01070.22980.1455-0.228800.23050.0038-0.0290.22670.00850.23097.217.6912.9761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 163 )A2 - 163
2X-RAY DIFFRACTION2chain 'A' and (resid 164 through 207 )A164 - 207
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 277 )A208 - 277
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 12 )B2 - 12
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 31 )B13 - 31
6X-RAY DIFFRACTION6chain 'B' and (resid 32 through 42 )B32 - 42
7X-RAY DIFFRACTION7chain 'B' and (resid 43 through 52 )B43 - 52
8X-RAY DIFFRACTION8chain 'B' and (resid 53 through 72 )B53 - 72
9X-RAY DIFFRACTION9chain 'B' and (resid 73 through 78 )B73 - 78
10X-RAY DIFFRACTION10chain 'B' and (resid 79 through 91 )B79 - 91
11X-RAY DIFFRACTION11chain 'B' and (resid 92 through 100 )B92 - 100
12X-RAY DIFFRACTION12chain 'C' and (resid 1 through 12 )C1 - 12

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