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- PDB-1xr8: Crystal Structures of HLA-B*1501 in Complex with Peptides from Hu... -

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Basic information

Entry
Database: PDB / ID: 1xr8
TitleCrystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3
Components
  • Beta-2-microglobulin
  • EBNA-3 nuclear protein
  • HLA class I histocompatibility antigen, B-15 alpha chain
KeywordsIMMUNE SYSTEM / major histocompatibility antigen / MHC / HLA / HLA-B62 / HLA-B*1501 / complex (antigen-peptide)
Function / homology
Function and homology information


host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 ...host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / : / : / secretory granule membrane / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / defense response / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / 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 / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / 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 / : ...Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UREA / HLA class I histocompatibility antigen, B alpha chain / Epstein-Barr nuclear antigen 3 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRoder, G. / Blicher, T. / Johannessen, B.R. / Kristensen, O. / Buus, S. / Gajhede, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype
Authors: Roder, G. / Blicher, T. / Justesen, S. / Johannesen, B. / Kristensen, O. / Kastrup, J. / Buus, S. / Gajhede, M.
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2005Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-15 alpha chain
B: Beta-2-microglobulin
C: EBNA-3 nuclear protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1717
Polymers44,7333
Non-polymers4384
Water4,053225
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.582, 81.891, 110.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, B-15 alpha chain / MHC class I antigen B*15 / HLA-B*1501


Mass: 31958.195 Da / Num. of mol.: 1 / Fragment: residues (1-276)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-Bw62.1 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P30464, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / HDCMA22P / beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide EBNA-3 nuclear protein / EBNA-3A


Mass: 1026.146 Da / Num. of mol.: 1 / Fragment: residues (274-282) / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: P12977

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Non-polymers , 4 types, 229 molecules

#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M MgAc4H20, 0.1M Na-cacodylate, pH 6.5, 20% w/v PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.969 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 28, 2004
RadiationMonochromator: Bent diamond crystal, horizontally focusing (R = 12 m)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.969 Å / Relative weight: 1
ReflectionResolution: 2.3→19.44 Å / Num. all: 20977 / Num. obs: 19549 / % possible obs: 93.19 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 29.855 Å2 / Rsym value: 0.104 / Net I/σ(I): 5.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.9 / Num. measured all: 10859 / Num. unique all: 2868 / Rsym value: 0.339 / % possible all: 96.29

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Processing

Software
NameVersionClassification
SCALAdata scaling
MOLREPphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A1M

1a1m


Resolution: 2.3→19.437 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 6.093 / SU ML: 0.152 / SU R Cruickshank DPI: 0.34 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUHGOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.252 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 997 5.1 %RANDOM
Rwork0.169 ---
all0.173 20977 --
obs0.173 19549 93.19 %-
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 23.975 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3155 0 29 225 3409
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.02232790.021
X-RAY DIFFRACTIONr_angle_refined_deg1.88944451.925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3023835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45417723.164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.553015
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8073215
X-RAY DIFFRACTIONr_chiral_restr0.1334470.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00925870.02
X-RAY DIFFRACTIONr_nbd_refined0.2213950.2
X-RAY DIFFRACTIONr_nbtor_refined0.30421430.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1742470.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.238370.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.134120.2
X-RAY DIFFRACTIONr_mcbond_it1.33319911.5
X-RAY DIFFRACTIONr_mcangle_it2.05831072
X-RAY DIFFRACTIONr_scbond_it3.20915183
X-RAY DIFFRACTIONr_scangle_it5.02613384.5
LS refinement shellResolution: 2.3→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 -74 %
Rwork0.171 1361 -
obs--96.76 %

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