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- PDB-3fqw: Phosphorylation of self-peptides alters Human Leukocyte Antigen C... -

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Basic information

Entry
Database: PDB / ID: 3fqw
TitlePhosphorylation of self-peptides alters Human Leukocyte Antigen Class I-restricted antigen presentation and generates tumor specific epitopes
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • peptide 1097-1105 from insulin receptor substrate 2 (IRS2): RVASPTSGV
KeywordsIMMUNE SYSTEM / PHOSPHORYLATION / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Polymorphism / Transmembrane / Ubl conjugation / Disease mutation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / cancer / TCR / self-epitope
Function / homology
Function and homology information


positive regulation of type B pancreatic cell proliferation / epithelial cell migration / negative regulation of long-chain fatty acid import across plasma membrane / IRS-related events triggered by IGF1R / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / type B pancreatic cell proliferation / Signaling by Erythropoietin / Erythropoietin activates STAT5 ...positive regulation of type B pancreatic cell proliferation / epithelial cell migration / negative regulation of long-chain fatty acid import across plasma membrane / IRS-related events triggered by IGF1R / IRS-mediated signalling / positive regulation of fatty acid beta-oxidation / phosphatidylinositol 3-kinase activator activity / type B pancreatic cell proliferation / Signaling by Erythropoietin / Erythropoietin activates STAT5 / Erythropoietin activates Phospholipase C gamma (PLCG) / mammary gland development / positive regulation of glucose metabolic process / transmembrane receptor protein tyrosine kinase adaptor activity / negative regulation of B cell apoptotic process / Signaling by Leptin / PI3K/AKT activation / positive regulation of mesenchymal cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / negative regulation of kinase activity / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / CD8 receptor binding / IRS activation / positive regulation of epithelial cell migration / antigen processing and presentation of exogenous peptide antigen via MHC class I / lipid homeostasis / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / regulation of lipid metabolic process / TAP binding / SOS-mediated signalling / RET signaling / protection from natural killer cell mediated cytotoxicity / PI3K Cascade / positive regulation of glycogen biosynthetic process / Signal attenuation / beta-2-microglobulin binding / phosphatidylinositol 3-kinase binding / response to glucose / T cell receptor binding / Erythropoietin activates RAS / detection of bacterium / Growth hormone receptor signaling / positive regulation of B cell proliferation / 14-3-3 protein binding / Interleukin-7 signaling / 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 / 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 / positive regulation of glucose import / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / cellular response to glucose stimulus / 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 / insulin receptor binding / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / positive regulation of insulin secretion / brain development / T cell mediated cytotoxicity / 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 / specific granule lumen / recycling endosome membrane / cellular response to insulin stimulus / phagocytic vesicle membrane / peptide antigen binding / glucose metabolic process / positive regulation of cellular senescence / Constitutive Signaling by Aberrant PI3K in Cancer / antigen processing and presentation of exogenous peptide antigen via MHC class II
Similarity search - Function
Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding domain / PH domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...Insulin receptor substrate / Phosphotyrosine-binding domain (IRS1-like) / IRS-type PTB domain profile. / IRS-type PTB domain / PTB domain (IRS-1 type) / Phosphotyrosine-binding domain / PH domain / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / PH-like domain superfamily / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / 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 / Insulin receptor substrate 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.927 Å
AuthorsPetersen, J. / Rossjohn, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2009
Title: Phosphorylated self-peptides alter human leukocyte antigen class I-restricted antigen presentation and generate tumor-specific epitopes
Authors: Petersen, J. / Wurzbacher, S.J. / Williamson, N.A. / Ramarathinam, S.H. / Reid, H.H. / Nair, A.K. / Zhao, A.Y. / Nastovska, R. / Rudge, G. / Rossjohn, J. / Purcell, A.W.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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, A-2 alpha chain
B: Beta-2-microglobulin
C: peptide 1097-1105 from insulin receptor substrate 2 (IRS2): RVASPTSGV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9849
Polymers44,3633
Non-polymers6216
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-50 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.982, 79.378, 111.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31854.203 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR DOMAINS ALPHA1, ALPHA2, ALPHA3, UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11635.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET 30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide peptide 1097-1105 from insulin receptor substrate 2 (IRS2): RVASPTSGV


Mass: 873.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q9Y4H2*PLUS

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Non-polymers , 3 types, 343 molecules

#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cd
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.81 % / Mosaicity: 0.456 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 13% PEG3350, 10mM CdCl2, 10mM CoCl2, 0.1M NaCl, pH7.4, temperature 293K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 8, 2008 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.927→50 Å / Num. obs: 38037 / % possible obs: 93.1 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.056 / Χ2: 1.014 / Net I/σ(I): 22.144
Reflection shellResolution: 1.93→2 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 3.7 / Num. unique all: 3049 / Χ2: 0.992 / % possible all: 75.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VLL

2vll


Resolution: 1.927→23.655 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.873 / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1885 4.96 %RANDOM
Rwork0.169 ---
obs0.17 38009 93.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.378 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 74.93 Å2 / Biso mean: 28.227 Å2 / Biso min: 8.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.321 Å20 Å2-0 Å2
2--2.371 Å20 Å2
3----1.049 Å2
Refinement stepCycle: LAST / Resolution: 1.927→23.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3148 0 6 338 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063246
X-RAY DIFFRACTIONf_angle_d1.0224414
X-RAY DIFFRACTIONf_chiral_restr0.075452
X-RAY DIFFRACTIONf_plane_restr0.004580
X-RAY DIFFRACTIONf_dihedral_angle_d15.211172
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.927-1.9790.2581030.2042116221972
1.979-2.0370.2371310.1842612274389
2.037-2.1030.1991460.1722756290294
2.103-2.1780.2021360.172777291394
2.178-2.2650.2421420.162790293294
2.265-2.3680.1971560.1662816297295
2.368-2.4930.2131320.1712820295295
2.493-2.6490.2221440.1812833297795
2.649-2.8530.2051550.1762866302196
2.853-3.140.1991590.172847300696
3.14-3.5930.2061700.1642887305797
3.593-4.5220.1531530.1362965311897
4.522-23.6570.1721580.1623039319796
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)
11.24280.0189-0.26970.75270.22421.0578-0.06890.118-0.0141-0.0457-0.05340.0962-0.0261-0.060.12010.1147-0.004-0.01270.0869-0.01770.13736.3075-11.8449-42.2309
20.65670.51420.1330.57650.32180.6182-0.03620.07520.0131-0.1184-0.0351-0.0062-0.06610.1620.04840.036-0.03070.01530.00760.0070.038119.837114.5541-20.8729
30.49370.4792-0.15010.17350.29041.1885-0.0161-0.1093-0.05960.2522-0.0272-0.03440.17620.01110.0420.24350.0190.01030.10720.0050.16398.0478-4.5285-15.8416
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1-181) or chain C
2X-RAY DIFFRACTION2(chain A and resseq 182-275)
3X-RAY DIFFRACTION3chain B

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