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- PDB-4no3: Crystal structure of AMPD2 phosphopeptide bound to HLA-A2 -

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Basic information

Entry
Database: PDB / ID: 4no3
TitleCrystal structure of AMPD2 phosphopeptide bound to HLA-A2
Components
  • AMP deaminase 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
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


cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / podocyte development / Purine salvage / GMP salvage / IMP salvage / GTP metabolic process ...cyclic purine nucleotide metabolic process / AMP deaminase / AMP deaminase activity / IMP biosynthetic process / AMP metabolic process / podocyte development / Purine salvage / GMP salvage / IMP salvage / GTP metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / detection of bacterium / ATP metabolic process / T cell receptor binding / energy homeostasis / cholesterol homeostasis / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of iron ion transport / lumenal side of endoplasmic reticulum membrane / T cell mediated cytotoxicity / cellular response to iron(III) ion / 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 / transferrin transport / regulation of iron ion transport / regulation of erythrocyte differentiation / negative regulation of receptor-mediated endocytosis / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of type II interferon production / phagocytic vesicle membrane / positive regulation of immune response / recycling endosome membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / T cell receptor signaling pathway / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane
Similarity search - Function
AMP deaminase / AMP deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Metal-dependent hydrolase / 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 ...AMP deaminase / AMP deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Metal-dependent hydrolase / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 / AMP deaminase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.703 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 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 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 1.3Sep 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_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: AMP deaminase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8907
Polymers44,6413
Non-polymers2484
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-7 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.000, 55.200, 75.100
Angle α, β, γ (deg.)90.00, 104.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#3: Protein/peptide AMP deaminase 2


Mass: 1168.237 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 165-173) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01433
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12% PEG3350, 8% tacsimate, pH 8.0, 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: Sep 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.703→20.052 Å / Num. obs: 46573 / % possible obs: 91.9 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 28.19 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 33.95
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.703-1.90.3284.684880810750175.4
1.9-20.14910.95256374833193.9
2-2.10.10115.94223654092197
2.1-2.40.06324.66517938778199.1
2.4-2.70.04140.964436253661100
2.7-30.03558.41373793427199.9
3-40.02677.87607145363199.9
4-50.02490.89218191936199.7
5-60.02589.679412848199.9
6-100.02590.1410346944199.9
10-20.0520.02491.132364236184.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3bh9


Resolution: 1.703→20.052 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2274 / WRfactor Rwork: 0.2037 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8383 / SU B: 2.327 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1279 / SU Rfree: 0.1175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2317 5 %RANDOM
Rwork0.208 ---
obs0.2091 46573 90.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 45.44 Å2 / Biso mean: 21.6785 Å2 / Biso min: 9.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.06 Å2
2---0.13 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.703→20.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 16 390 3552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213249
X-RAY DIFFRACTIONr_angle_refined_deg1.1111.9274402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5685381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7223.081172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15215.028530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1691529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212536
X-RAY DIFFRACTIONr_mcbond_it0.5251.51913
X-RAY DIFFRACTIONr_mcangle_it1.00523087
X-RAY DIFFRACTIONr_scbond_it1.46231336
X-RAY DIFFRACTIONr_scangle_it2.4724.51315
LS refinement shellResolution: 1.703→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 66 -
Rwork0.309 1218 -
all-1284 -
obs--34.58 %

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