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- PDB-7mja: HLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide -

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Basic information

Entry
Database: PDB / ID: 7mja
TitleHLA-A*24:02 bound to Neuroblastoma derived PHOX2B peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen
  • Paired mesoderm homeobox protein 2B peptide
KeywordsIMMUNE SYSTEM / NEUROBLASTOMA TUMOR ANTIGEN / PHOX2B / IGFBPL1 / HUMAN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I / MHC-I / COMPLEX
Function / homology
Function and homology information


medullary reticular formation development / autonomic nervous system development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / hindbrain tangential cell migration ...medullary reticular formation development / autonomic nervous system development / parasympathetic nervous system development / efferent axon development in a lateral line nerve / retrotrapezoid nucleus neuron differentiation / negative regulation of type B pancreatic cell proliferation / noradrenergic neuron development / cell differentiation in hindbrain / respiratory system development / hindbrain tangential cell migration / cellular response to carbon dioxide / noradrenergic neuron differentiation / brainstem development / regulation of respiratory gaseous exchange by nervous system process / motor neuron migration / sympathetic ganglion development / enteric nervous system development / neural crest cell migration involved in autonomic nervous system development / glial cell differentiation / type B pancreatic cell proliferation / sympathetic nervous system development / cellular response to BMP stimulus / dopaminergic neuron differentiation / skeletal muscle cell differentiation / inner ear development / membrane depolarization / antigen processing and presentation / negative regulation of neuron differentiation / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of neuron differentiation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / response to activity / 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 / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / RNA polymerase II transcription regulatory region sequence-specific DNA binding / neuron migration / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / sensory perception of smell / sequence-specific double-stranded DNA binding / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of cold-induced thermogenesis / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein refolding / early endosome membrane / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / membrane => GO:0016020 / learning or memory / DNA-binding transcription factor activity, RNA polymerase II-specific / immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 ...Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Homeobox-like domain 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 / Immunoglobulin-like fold
Similarity search - Domain/homology
Beta-2-microglobulin / HLA class I histocompatibility antigen / Paired mesoderm homeobox protein 2B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 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: HLA class I histocompatibility antigen
B: Beta-2-microglobulin
C: Paired mesoderm homeobox protein 2B peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5794
Polymers45,4863
Non-polymers921
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-21 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.211, 77.211, 174.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / HLA-A protein / MHC class I antigen / MHC ...HLA class I histocompatibility antigen A alpha chain / HLA-A protein / MHC class I antigen / MHC class I protein / MHC leukocyte antigen / Major histocompatibility complex / class I / A


Mass: 32466.869 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA, HLA-A*24 :02 variant, HLA-A*24:02 VARIANT / Production host: Escherichia coli (E. coli) / References: UniProt: Q95J06
#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 Paired mesoderm homeobox protein 2B peptide / Neuroblastoma Phox / NBPhox / PHOX2B homeodomain protein / Paired-like homeobox 2B


Mass: 1140.268 Da / Num. of mol.: 1 / Fragment: Residues 43-51 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q99453
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.86 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 10% 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 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 Å / Relative weight: 1
ReflectionResolution: 1.69→87.43 Å / Num. obs: 60180 / % possible obs: 100 % / Redundancy: 25.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.109 / Net I/σ(I): 18.4
Reflection shellResolution: 1.69→1.72 Å / Rmerge(I) obs: 0.671 / Mean I/σ(I) obs: 4.8 / Num. unique obs: 3045 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VXN

3vxn


Resolution: 1.69→57.875 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 2000 3.33 %
Rwork0.1746 --
obs0.1754 60060 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.69→57.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3130 0 6 368 3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153220
X-RAY DIFFRACTIONf_angle_d1.2284362
X-RAY DIFFRACTIONf_dihedral_angle_d6.6381908
X-RAY DIFFRACTIONf_chiral_restr0.058443
X-RAY DIFFRACTIONf_plane_restr0.007574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6901-1.73230.22961400.19454069X-RAY DIFFRACTION100
1.7323-1.77920.25361410.19364070X-RAY DIFFRACTION100
1.7792-1.83150.24311400.19264075X-RAY DIFFRACTION100
1.8315-1.89060.23761410.18544095X-RAY DIFFRACTION100
1.8906-1.95820.20261400.17314070X-RAY DIFFRACTION100
1.9582-2.03660.21171420.16584111X-RAY DIFFRACTION100
2.0366-2.12930.18291410.17514085X-RAY DIFFRACTION100
2.1293-2.24160.1821410.17324132X-RAY DIFFRACTION100
2.2416-2.3820.2021430.17794119X-RAY DIFFRACTION100
2.382-2.5660.22771430.17744151X-RAY DIFFRACTION100
2.566-2.82420.1771430.17754153X-RAY DIFFRACTION100
2.8242-3.23280.20171440.17784208X-RAY DIFFRACTION100
3.2328-4.07290.191470.16574249X-RAY DIFFRACTION100
4.0729-57.80.19051540.1724473X-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)
10.7526-0.407-0.26362.07280.99382.48010.04820.08-0.09030.1053-0.17460.21770.1737-0.28910.10830.1463-0.04410.00670.1613-0.04270.19849.23635.1713195.3518
21.23931.5021.0034.45543.60533.1270.0469-0.05-0.10180.724-0.12210.15390.8052-0.31830.20630.3433-0.06960.04710.142-0.00570.19099.56933.0453207.1912
32.3107-2.5749-2.50743.7652.90313.67230.2152-0.02030.13940.0450.0106-0.2582-0.0120.1244-0.26620.1452-0.0166-0.01290.163-0.03260.211919.359941.1414203.4697
41.6222-0.5766-0.25013.21170.61221.70030.103-0.16340.00520.55420.1132-0.49820.02760.4425-0.16080.2318-0.0156-0.10460.1971-0.06790.253124.894543.1547212.4558
50.5328-0.21250.10052.0130.73180.26720.04770.0385-0.0006-0.3741-0.0772-0.14240.17470.13770.09590.10250.00380.00580.1496-0.0320.171221.418138.6037185.1956
60.78830.21850.09752.1101-0.64980.7258-0.02820.14520.0536-0.6683-0.0679-0.2284-0.15580.10530.08190.45890.00180.07140.1709-0.00710.197622.274256.4995172.6612
71.30220.67460.97893.02842.91263.33850.0324-0.00420.0385-0.3534-0.21540.2071-0.5007-0.07580.24640.22290.0224-0.01740.1482-0.00890.2139.184356.1588190.0079
81.4389-0.73540.34290.5289-0.17670.09460.01920.49070.026-0.58040.06220.2620.176-0.4633-0.10940.70570.1513-0.23440.3841-0.02760.23553.460148.6435168.3722
92.24390.4961.25111.68420.88546.02020.20010.2019-0.0865-0.3743-0.08080.3480.2025-0.1176-0.01740.29530.0532-0.07850.1689-0.04090.2545.427349.9887183.1109
106.0387-0.53226.47810.9135-1.44057.81310.1858-0.05910.0055-0.1173-0.06070.5705-0.1336-0.6744-0.14870.20350.0819-0.07360.2952-0.04280.3546-2.859453.4658188.7805
112.44410.39431.8240.2617-0.68226.18790.1140.6009-0.6814-0.48220.11130.89490.032-0.7086-0.12150.2058-0.0349-0.16780.3838-0.00390.5143-4.707444.3234185.539
121.6083-0.13580.90342.4484-0.37325.29730.0680.1919-0.0998-0.3130.04110.2456-0.03920.0098-0.14460.13860.0016-0.02340.142-0.04040.18658.086646.6168189.405
132.01380.72480.65950.2793-0.11357.07010.17580.13860.3444-0.49020.09060.4963-0.2347-0.6044-0.14030.49560.1709-0.21010.3336-0.0020.4243-3.634557.0237177.7296
145.24180.93522.04262.23053.59586.4247-0.08860.05170.9095-0.1138-0.24350.2825-0.5872-0.31830.12770.23470.0710.01280.2393-0.02850.37551.48561.6265196.9537
154.7101-0.9173-3.26394.94090.7546.86490.21080.4080.2541-0.677-0.02180.3617-0.5365-0.2807-0.13920.41960.0935-0.11690.1943-0.00080.29443.622959.6948177.546
161.51370.17150.3914.4823.20612.4014-0.1295-0.07350.05050.87620.2249-0.02880.7942-0.0154-0.05680.31320.0208-0.01430.1571-0.02360.164616.246431.8577207.4481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 57 )A2 - 57
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 85 )A58 - 85
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 119 )A86 - 119
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 150 )A120 - 150
5X-RAY DIFFRACTION5chain 'A' and (resid 151 through 197 )A151 - 197
6X-RAY DIFFRACTION6chain 'A' and (resid 198 through 274 )A198 - 274
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 12 )B2 - 12
8X-RAY DIFFRACTION8chain 'B' and (resid 13 through 20 )B13 - 20
9X-RAY DIFFRACTION9chain 'B' and (resid 21 through 30 )B21 - 30
10X-RAY DIFFRACTION10chain 'B' and (resid 31 through 46 )B31 - 46
11X-RAY DIFFRACTION11chain 'B' and (resid 47 through 51 )B47 - 51
12X-RAY DIFFRACTION12chain 'B' and (resid 52 through 71 )B52 - 71
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 83 )B72 - 83
14X-RAY DIFFRACTION14chain 'B' and (resid 84 through 90 )B84 - 90
15X-RAY DIFFRACTION15chain 'B' and (resid 91 through 99 )B91 - 99
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 9 )C1 - 9

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