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- PDB-4no2: Crystal structure of RQA_V phosphopeptide bound to HLA-A2 -

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Basic information

Entry
Database: PDB / ID: 4no2
TitleCrystal structure of RQA_V phosphopeptide bound to HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Lymphocyte-specific protein 1
KeywordsIMMUNE SYSTEM/ANTIGEN / Phosphoserine / phosphopeptide / peptide-MHC complex / MHC / tumor immunology / peptide conformation / post translational modification / tumor antigen / neoepitope / IMMUNE SYSTEM-ANTIGEN complex
Function / homology
Function and homology information


cellular response to interleukin-7 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...cellular response to interleukin-7 / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / 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 / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / detection of bacterium / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / 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 / 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 / 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 / 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 / chemotaxis / 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 / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / actin cytoskeleton / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / actin binding / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / endoplasmic reticulum membrane
Similarity search - Function
Lymphocyte-specific protein / Caldesmon/lymphocyte specific protein / Caldesmon / 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 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Lymphocyte-specific protein / Caldesmon/lymphocyte specific protein / Caldesmon / 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 / 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. / 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 / Lymphocyte-specific protein 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMohammed, F. / Stones, D.H. / Willcox, B.E.
CitationJournal: Oncotarget / Year: 2017
Title: The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.
Authors: Mohammed, F. / Stones, D.H. / Zarling, A.L. / Willcox, C.R. / Shabanowitz, J. / Cummings, K.L. / Hunt, D.F. / Cobbold, M. / Engelhard, V.H. / Willcox, B.E.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.3May 29, 2019Group: Data collection / Database references / Derived calculations
Category: citation / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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: Lymphocyte-specific protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0657
Polymers44,8563
Non-polymers2094
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-23 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.200, 54.700, 75.200
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number5
Space group name H-MC121

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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 / Class I histocompatibility antigen A*0201


Mass: 31725.088 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 25-298)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 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 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Lymphocyte-specific protein 1 / 47 kDa actin-binding protein / 52 kDa phosphoprotein / pp52 / Lymphocyte-specific antigen WP34


Mass: 1382.499 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 249-260) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P33241

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Non-polymers , 3 types, 260 molecules

#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG8000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2→19.865 Å / Num. obs: 31595 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 31.088 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 32.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.10.4654.35275194172196.1
2.1-2.20.3186.39236403498197.7
2.2-2.30.2869.05202192915198.9
2.3-2.40.20310.57188142487199.9
2.4-2.70.12617.86532575477199.9
2.7-30.08131.35456783530199.8
3-40.04160.967394254611100
4-50.02494.71269991980199.6
5-60.02496.4411804872199.5
6-100.02397.95128089601100
10-19.8650.02114.753024243185.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BH9

3bh9


Resolution: 2→19.865 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.2218 / WRfactor Rwork: 0.1894 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8276 / SU B: 4.291 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1928 / SU Rfree: 0.1707 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 1576 5 %RANDOM
Rwork0.2079 ---
obs0.2098 31585 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.26 Å2 / Biso mean: 26.7458 Å2 / Biso min: 11.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å2-0.91 Å2
2--0.33 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2→19.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 13 256 3430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0213220
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9234372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62623.018169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8315.03500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0041528
X-RAY DIFFRACTIONr_chiral_restr0.0840.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022533
X-RAY DIFFRACTIONr_nbd_refined0.1890.21192
X-RAY DIFFRACTIONr_nbtor_refined0.2890.22118
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2180
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1190.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.29
X-RAY DIFFRACTIONr_mcbond_it0.6541.51920
X-RAY DIFFRACTIONr_mcangle_it1.25923083
X-RAY DIFFRACTIONr_scbond_it1.87631332
X-RAY DIFFRACTIONr_scangle_it3.054.51289
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 117 -
Rwork0.252 2158 -
all-2275 -
obs--95.51 %

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