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- PDB-4pg2: The crystal structure of H-2Db with a S-glutathionylated peptide -

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Basic information

Entry
Database: PDB / ID: 4pg2
TitleThe crystal structure of H-2Db with a S-glutathionylated peptide
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • CYS-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / Immune receptor / glutathionylated peptide / T cell Biology / antigen presentation
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / endocytosis involved in viral entry into host cell / 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 / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation
Similarity search - Function
Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 ...Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / 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 / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / 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
GLUTATHIONE / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Spike glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTheodossis, A. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The cellular redox environment alters antigen presentation.
Authors: Trujillo, J.A. / Croft, N.P. / Dudek, N.L. / Channappanavar, R. / Theodossis, A. / Webb, A.I. / Dunstone, M.A. / Illing, P.T. / Butler, N.S. / Fett, C. / Tscharke, D.C. / Rossjohn, J. / ...Authors: Trujillo, J.A. / Croft, N.P. / Dudek, N.L. / Channappanavar, R. / Theodossis, A. / Webb, A.I. / Dunstone, M.A. / Illing, P.T. / Butler, N.S. / Fett, C. / Tscharke, D.C. / Rossjohn, J. / Perlman, S. / Purcell, A.W.
History
DepositionMay 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Structure summary
Revision 1.2Oct 15, 2014Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Feb 14, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
C: Beta-2-microglobulin
D: CYS-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5018
Polymers44,8093
Non-polymers6925
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-37 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.699, 79.099, 85.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 31990.590 Da / Num. of mol.: 1 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11791.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules D

#3: Protein/peptide CYS-SER-LEU-TRP-ASN-GLY-PRO-HIS-LEU


Mass: 1027.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q02385*PLUS

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Non-polymers , 3 types, 24 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M citrate pH7.5, 28% PEG 3350, 0.2M LiSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 28, 2012
RadiationMonochromator: Cu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→16 Å / Num. obs: 11701 / % possible obs: 87.9 % / Redundancy: 4 % / Net I/σ(I): 10.5

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Processing

SoftwareName: REFMAC / Version: 5.5.0088 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→15.86 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.9 / SU B: 32.314 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26668 1176 10.2 %RANDOM
Rwork0.20819 ---
obs0.21399 10373 87.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å2-0 Å2
2--4.41 Å20 Å2
3----3.31 Å2
Refinement stepCycle: 1 / Resolution: 2.8→15.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2958 0 40 19 3017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0213087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.9414199
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5285357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85623.526156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61115478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.441521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212410
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2961.51813
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.57422916
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.9231274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5024.51283
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 68 -
Rwork0.3 781 -
obs--91.59 %
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)
12.45771.2676-0.30733.5251-1.23864.22080.0970.12670.1804-0.09260.01020.1685-0.33670.5037-0.10720.0576-0.0327-0.01160.1468-0.03670.0674-25.393-23.942-17.932
213.5572.4883-0.87617.7236-0.9666.9020.0265-0.4168-0.82050.42050.0492-1.12710.13860.9708-0.07580.0767-0.06370.01720.3459-0.18410.39872.624-15.5291.25
34.45312.5976-0.13945.66673.05676.93070.3651-0.18810.42010.80550.10250.2008-0.38560.0681-0.46760.3195-0.02240.10510.1274-0.0370.1485-17.123-16.368.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 180
2X-RAY DIFFRACTION1D1 - 9
3X-RAY DIFFRACTION1A303
4X-RAY DIFFRACTION2A181 - 275
5X-RAY DIFFRACTION3C0 - 99

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