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- PDB-3bh8: Crystal Structure of RQA_M Phosphopeptide Bound to HUMAN Class I ... -

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Basic information

Entry
Database: PDB / ID: 3bh8
TitleCrystal Structure of RQA_M Phosphopeptide Bound to HUMAN Class I MHC HLA-A2
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • decameric peptide from Lymphocyte-specific protein 1
KeywordsIMMUNE SYSTEM / PHOSPHOSERINE / PHOSPHOPEPTIDE / MHC / HLA-A2 / ANCHOR RESIDUE / TUMOR ANTIGEN / GLYCOPROTEIN / HOST-VIRUS INTERACTION / IMMUNE RESPONSE / MHC I / POLYMORPHISM / TRANSMEMBRANE / UBL CONJUGATION / IMMUNOGLOBULIN DOMAIN / PHOSPHOPROTEIN
Function / homology
Function and homology information


cellular response to interleukin-7 / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / 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 / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / 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 / cellular defense response / detection of bacterium / T cell receptor binding / 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 / 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 / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / chemotaxis / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / actin cytoskeleton / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / actin binding / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum
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 / 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 / Lymphocyte-specific protein 1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMohammed, F. / Cobbold, M. / Zarling, A.L. / Salim, M. / Barrett-Wilt, G.A. / Shabanowitz, J. / Hunt, D.F. / Engelhard, V.H. / Willcox, B.E.
CitationJournal: Nat.Immunol. / Year: 2008
Title: Phosphorylation-dependent interaction between antigenic peptides and MHC class I: a molecular basis for the presentation of transformed self
Authors: Mohammed, F. / Cobbold, M. / Zarling, A.L. / Salim, M. / Barrett-Wilt, G.A. / Shabanowitz, J. / Hunt, D.F. / Engelhard, V.H. / Willcox, B.E.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: decameric peptide from Lymphocyte-specific protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9415
Polymers44,8173
Non-polymers1242
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-15 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.600, 55.100, 75.900
Angle α, β, γ (deg.)90.000, 103.500, 90.000
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


Mass: 31725.088 Da / Num. of mol.: 1 / Fragment: Alpha-1, Alpha-2, Alpha-3
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: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769
#3: Protein/peptide decameric peptide from Lymphocyte-specific protein 1 / Protein pp52 / 52 kDa phosphoprotein / Lymphocyte-specific antigen WP34 / 47 kDa actin-binding protein


Mass: 1212.290 Da / Num. of mol.: 1 / Fragment: UNP residues 249-258 / Source method: obtained synthetically / Details: COMMERCIAL SYNTHESIS / References: UniProt: P33241
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG 8000, 0.1M 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: SATURN / Detector: CCD / Date: Apr 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 53891 / % possible obs: 90 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 25.593 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 26.79
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.70.7032.330745670667.6
1.7-1.80.468435020654483.7
1.8-1.90.2976.631325560589.2
1.9-20.18210.627025469592.8
2-2.10.1171523476396995.5
2.1-2.40.08521.451164852497.6
2.4-2.70.053234845526099.7
2.7-30.03746.627934338099.8
3-40.02573.158951529699.9
4-50.0292.2227361894100
5-60.0291.81023385299.9
6-100.0290.81093193199.9
100.01798.1255823585.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.006 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2560 5.1 %RANDOM
Rwork0.2 ---
obs0.202 50642 92.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.944 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-0.08 Å2
2---0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3166 0 8 368 3542
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213229
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9244386
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7775381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10423.059170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62715.029514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.231528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022533
X-RAY DIFFRACTIONr_nbd_refined0.1950.21319
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22141
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2234
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.214
X-RAY DIFFRACTIONr_mcbond_it0.9181.51983
X-RAY DIFFRACTIONr_mcangle_it1.40523087
X-RAY DIFFRACTIONr_scbond_it2.23331470
X-RAY DIFFRACTIONr_scangle_it3.4124.51299
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 147 -
Rwork0.279 2814 -
all-2961 -
obs--74.58 %

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