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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-microglobulinBeta-2 microglobulin
  • HLA-B35
KeywordsIMMUNE SYSTEM / gene regulation
Function / homology
Function and homology information


linoleic acid epoxygenase activity / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / Xenobiotics / regulation of interleukin-12 production / regulation of dendritic cell differentiation / 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 T cell anergy ...linoleic acid epoxygenase activity / arachidonic acid epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / Xenobiotics / regulation of interleukin-12 production / regulation of dendritic cell differentiation / 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 T cell anergy / retinoic acid metabolic process / regulation of interleukin-6 production / retinol metabolic process / unspecific monooxygenase / aromatase activity / 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 / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / monooxygenase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / defense response / ER to Golgi transport vesicle membrane / response to molecule of bacterial origin / 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 / oxygen binding / 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 / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / iron ion binding / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / intracellular membrane-bounded organelle / heme binding / Neutrophil degranulation
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 ...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 / Immunoglobulins / Immunoglobulin-like fold / 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

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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 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 / Water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 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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