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- PDB-3ox8: Crystal Structure of HLA A*02:03 Bound to HBV Core 18-27 -

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Basic information

Entry
Database: PDB / ID: 3ox8
TitleCrystal Structure of HLA A*02:03 Bound to HBV Core 18-27
Components
  • 10mer peptide from Pre-core-protein
  • Beta-2-microglobulin
  • MHC class I antigen
KeywordsIMMUNE SYSTEM / Protein-Peptide Complex / Host-virus interaction / Immunogenicity / Therapeutic Design / TCR Recognition / Helix / Beta-sheet / Antigen Presentation / Peptide Binding / Cell Surface
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / antigen processing and presentation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / antigen processing and presentation / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / viral penetration into host nucleus / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / 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 / Modulation by Mtb of host immune system / host cell / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / membrane => GO:0016020 / learning or memory / symbiont entry into host cell / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / focal adhesion / virus-mediated perturbation of host defense response / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / 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 ...Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
External core antigen / Beta-2-microglobulin / HLA class I histocompatibility antigen A alpha chain / External core antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / Resolution: 2.16 Å
AuthorsLiu, J. / Chen, Y. / Lai, L. / Ren, E.
CitationJournal: Eur.J.Immunol. / Year: 2011
Title: Structural insights into the binding of hepatitis B virus core peptide to HLA-A2 alleles: Towards designing better vaccines.
Authors: Liu, J. / Chen, K.Y. / Ren, E.C.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: 10mer peptide from Pre-core-protein
D: MHC class I antigen
E: Beta-2-microglobulin
F: 10mer peptide from Pre-core-protein


Theoretical massNumber of molelcules
Total (without water)90,0446
Polymers90,0446
Non-polymers00
Water8,107450
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: 10mer peptide from Pre-core-protein


Theoretical massNumber of molelcules
Total (without water)45,0223
Polymers45,0223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-20 kcal/mol
Surface area18890 Å2
MethodPISA
2
D: MHC class I antigen
E: Beta-2-microglobulin
F: 10mer peptide from Pre-core-protein


Theoretical massNumber of molelcules
Total (without water)45,0223
Polymers45,0223
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-20 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.279, 68.269, 68.318
Angle α, β, γ (deg.)70.20, 84.40, 84.45
Int Tables number1
Space group name H-MP1

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Components

#1: Protein MHC class I antigen / CLASS I HISTOCOMPATIBILITY ANTIGEN


Mass: 31987.262 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, MHC HLA-A*02:03 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2LC95
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, BETA 2-MICROGLOBULIN, CDABP0092, HDCMA22P / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide 10mer peptide from Pre-core-protein


Mass: 1155.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Hepatitis B Virus Core 18-27 is synthesized. / Source: (synth.) Hepatitis B virus / References: UniProt: Q9YJW5, UniProt: P0C6H2*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPSE pH7.5, 1.4M sodium citrate tribasic dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→64.12 Å / Num. obs: 68748 / % possible obs: 95.76 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 11.062 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 4.68
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.16-2.221.710.34492.13517180.7
2.22-2.282.220.342.433534189.8
2.28-2.342.90.31192.973457197.7
2.34-2.413.610.28263.73681199.9
2.41-2.483.930.27014.232921100
2.48-2.564.390.24734.9333331100
2.56-2.654.710.23115.7332841100
2.65-2.764.740.2166.3734341100
2.76-2.894.720.18527.7734661100
2.89-3.054.710.16449.2633871100
3.05-3.244.70.137111.4132441100

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
AMoREphasing
REFMAC5.5.0102refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementResolution: 2.16→64.12 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.901 / SU B: 4.614 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23409 2733 5.1 %RANDOM
Rwork0.18221 ---
obs0.1848 50693 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 18.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.06 Å20.03 Å2
2--0 Å2-0.02 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.16→64.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6354 0 0 450 6804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0216566
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.928916
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8245768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76423.073358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.434151060
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5041558
X-RAY DIFFRACTIONr_chiral_restr0.1250.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0215202
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_it1.621.53846
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.76226208
X-RAY DIFFRACTIONr_scbond_it4.46232720
X-RAY DIFFRACTIONr_scangle_it6.6694.52706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 179 -
Rwork0.23 3171 -
obs--82.15 %

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