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- PDB-2cik: Insights Into Crossreactivity in Human Allorecognition: The Struc... -

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Entry
Database: PDB / ID: 2cik
TitleInsights Into Crossreactivity in Human Allorecognition: The Structure of HLA-B35011 Presenting an Epitope derived from Cytochrome P450.
Components
  • BETA-2-MICROGLOBULIN
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B-35 ALPHA CHAIN
  • PEPTIDE
KeywordsIMMUNE SYSTEM/PEPTIDE / ANTIGEN-PEPTIDE COMPLEX / MAJOR HISTOCOMPATIBILITY ANTIGEN / HUMAN / MHC / HLA / HLA-B3501 / EBV / ALLO-LIGAND / GLYCOPROTEIN / IMMUNE RESPONSE / MEMBRANE / MHC I / POLYMORPHISM / TRANSMEMBRANE / IMMUNOGLOBULIN DOMAIN / PYRROLIDONE CARBOXYLIC ACID / IMMUNE SYSTEM-PEPTIDE complex
Function / homology
Function and homology information


linoleic acid epoxygenase activity / organic acid metabolic process / arachidonate epoxygenase activity / arachidonate metabolic process / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / regulation of interleukin-12 production / Xenobiotics / regulation of dendritic cell differentiation / regulation of T cell anergy ...linoleic acid epoxygenase activity / organic acid metabolic process / arachidonate epoxygenase activity / arachidonate metabolic process / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / regulation of interleukin-12 production / Xenobiotics / regulation of dendritic cell differentiation / regulation of T cell anergy / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / regulation of interleukin-6 production / retinoic acid metabolic process / retinol metabolic process / unspecific monooxygenase / TAP binding / 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 / detection of bacterium / xenobiotic metabolic process / secretory granule membrane / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / monooxygenase activity / 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 / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / oxygen binding / 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 / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / 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 / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / iron ion binding / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
: / Cytochrome P450, E-class, group I / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Cytochrome P450 / Cytochrome P450 superfamily ...: / Cytochrome P450, E-class, group I / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / 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-B35 / HLA class I histocompatibility antigen, B alpha chain / Cytochrome P450 2C18 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A.
CitationJournal: Eur.J.Immunol. / Year: 2006
Title: The Structure of the Human Allo-Ligand Hla-B3501 in Complex with a Cytochrome P450 Peptide: Steric Hindrance Influences Tcr Allo-Recognition.
Authors: Hourigan, C.S. / Harkiolaki, M. / Peterson, N.A. / Bell, J.I. / Jones, E.Y. / O'Callaghan, C.A.
History
DepositionMar 22, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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 B-35 ALPHA CHAIN
B: BETA-2-MICROGLOBULIN
C: PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9926
Polymers44,7163
Non-polymers2763
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)51.320, 82.250, 109.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B-35 ALPHA CHAIN / HLA-B3501 / MHC CLASS I ANTIGEN B*35 / HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B3501 HEAVY CHAIN / ...HLA-B3501 / MHC CLASS I ANTIGEN B*35 / HLA CLASS I HISTOCOMPATIBILITY ANTIGEN B3501 HEAVY CHAIN / B350101 / B35011 / B35 / B35 / B3501


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGM-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / Variant (production host): (DE3)PLYSS / References: UniProt: P30685, UniProt: O19626*PLUS
#2: Protein BETA-2-MICROGLOBULIN / B2M


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGM-T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL-21 / Variant (production host): (DE3)PLYSS / References: UniProt: P61769
#3: Protein/peptide PEPTIDE


Mass: 1027.259 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: PEPTIDE EPITOPE FROM HUMAN CYTOCHROME P450 ISOFORMS IIC8, IIC9, IIC10 AND IIC18
Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P33260*PLUS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM BETA-2-MICROGLOBULIN IS THE ...INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM BETA-2-MICROGLOBULIN IS THE BETA-CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES
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: 2.6 Å3/Da / Density % sol: 53 % / Description: MODEL 1A1N WITH CHAIN C AND WATERS REMOVED.
Crystal growpH: 5.6
Details: 0.105M AMMONIUM ACETATE, 0.0525M TRI-SODIUM CITRATE DIHYDRATE PH 5.6 AND 15.75% W/V PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: May 30, 2001 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.75→20 Å / Num. obs: 47620 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 7.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.9
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A1N

1a1n


Resolution: 1.75→19.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.236 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1852 4 %RANDOM
Rwork0.197 ---
obs0.198 44265 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å20 Å20 Å2
2---0.27 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 18 325 3499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213265
X-RAY DIFFRACTIONr_bond_other_d0.0020.022272
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.944434
X-RAY DIFFRACTIONr_angle_other_deg0.8663.0025456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.015381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23823.182176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73715525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7991531
X-RAY DIFFRACTIONr_chiral_restr0.0820.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02709
X-RAY DIFFRACTIONr_nbd_refined0.2130.2528
X-RAY DIFFRACTIONr_nbd_other0.2050.22330
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21510
X-RAY DIFFRACTIONr_nbtor_other0.0820.21717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2227
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1841.52484
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26923107
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13431611
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0454.51327
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: 1.75→1.8 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 123
Rwork0.225 2954

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