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- PDB-2h6p: Crystal structure of HLA-B*3501 presenting the human cytochrome P... -

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Basic information

Entry
Database: PDB / ID: 2h6p
TitleCrystal structure of HLA-B*3501 presenting the human cytochrome P450 derived peptide, KPIVVLHGY
Components
  • 9 mer peptide from Cytochrome P450
  • Beta-2-microglobulin
  • HLA-B35
KeywordsIMMUNE SYSTEM / gene regulation
Function / homology
Function and homology information


linoleic acid epoxygenase activity / arachidonate epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / regulation of interleukin-12 production / Xenobiotics / regulation of dendritic cell differentiation / retinoic acid metabolic process / 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 ...linoleic acid epoxygenase activity / arachidonate epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / regulation of interleukin-12 production / Xenobiotics / regulation of dendritic cell differentiation / retinoic acid metabolic process / 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 / retinol metabolic process / unspecific monooxygenase / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of peptide antigen via MHC class I / MHC class Ib protein complex / TAP binding / detection of bacterium / 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 / xenobiotic catabolic process / beta-2-microglobulin binding / xenobiotic metabolic process / regulation of natural killer cell mediated immunity / positive regulation of T cell mediated cytotoxicity / early endosome lumen / secretory granule membrane / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / monooxygenase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / defense response / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / oxygen binding / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / specific granule lumen / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Interferon alpha/beta signaling / tertiary granule lumen / Modulation by Mtb of host immune system / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / protein-folding chaperone binding / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / iron ion binding / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / lysosomal membrane / heme binding / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region
Similarity search - Function
: / Cytochrome P450, E-class, group I / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily ...: / Cytochrome P450, E-class, group I / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArchbold, J.K. / Macdonald, W.A. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Alloreactivity between disparate cognate and allogeneic pMHC-I complexes is the result of highly focused, peptide-dependent structural mimicry
Authors: Archbold, J.K. / Macdonald, W.A. / Miles, J.J. / Brennan, R.M. / Kjer-Nielsen, L. / McCluskey, J. / Burrows, S.R. / Rossjohn, J.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA-B35
B: Beta-2-microglobulin
C: 9 mer peptide from Cytochrome P450


Theoretical massNumber of molelcules
Total (without water)44,7163
Polymers44,7163
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-21 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.279, 82.070, 109.881
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-B35 / HLA class I histocompatibility antigen / B-35 alpha chain


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: Extracellular domains alpha 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: O19626, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P61769
#3: Protein/peptide 9 mer peptide from Cytochrome P450 / CYPIIC18 / P450-6B/29C


Mass: 1027.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P33260
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 18% PEG 3350, 0.1M ammonium acetate, 0.1M cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→65.8 Å / Num. obs: 36699
Reflection shellResolution: 1.9→1.97 Å / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→65.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.191 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.9 / ESU R: 0.17 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23914 1831 5 %RANDOM
Rwork0.20985 ---
obs0.21133 34808 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 0 401 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213247
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9354414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0295381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39323.182176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56115525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9091531
X-RAY DIFFRACTIONr_chiral_restr0.060.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022573
X-RAY DIFFRACTIONr_nbd_refined0.1560.21417
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0720.2343
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.224
X-RAY DIFFRACTIONr_mcbond_it0.70232003
X-RAY DIFFRACTIONr_mcangle_it1.08253103
X-RAY DIFFRACTIONr_scbond_it1.68771481
X-RAY DIFFRACTIONr_scangle_it2.461101311
LS refinement shellResolution: 1.897→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 114 -
Rwork0.321 2002 -
obs--79.34 %
Refinement TLS params.Method: refined / Origin x: 12.957 Å / Origin y: 9.604 Å / Origin z: 36.048 Å
111213212223313233
T-0.1266 Å20.0021 Å2-0.0079 Å2--0.0929 Å2-0.0131 Å2---0.1839 Å2
L1.1321 °2-0.2786 °2-0.3177 °2-0.7796 °2-0.2119 °2--0.6014 °2
S-0.0557 Å °-0.0383 Å °-0.0919 Å °0.0392 Å °0.0343 Å °0.0029 Å °-0.0015 Å °-0.0423 Å °0.0214 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2761 - 276
2X-RAY DIFFRACTION1BB1 - 991 - 99
3X-RAY DIFFRACTION1CC1 - 91 - 9

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