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- PDB-1xr9: Crystal Structures of HLA-B*1501 in Complex with Peptides from Hu... -

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Basic information

Entry
Database: PDB / ID: 1xr9
TitleCrystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-15 alpha chain
  • Ubiquitin-conjugating enzyme E2 E1
KeywordsIMMUNE SYSTEM/Ligase / major histocompatibility antigen / MHC / HLA / HLA-B62 / HLA-B*1501 / complex (antigen-peptide) / IMMUNE SYSTEM-Ligase COMPLEX
Function / homology
Function and homology information


ISG15 transferase activity / ISG15-protein conjugation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / (E3-independent) E2 ubiquitin-conjugating enzyme / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...ISG15 transferase activity / ISG15-protein conjugation / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / Aberrant regulation of mitotic exit in cancer due to RB1 defects / Phosphorylation of the APC/C / (E3-independent) E2 ubiquitin-conjugating enzyme / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / E2 ubiquitin-conjugating enzyme / Regulation of APC/C activators between G1/S and early anaphase / ubiquitin conjugating enzyme activity / protection from natural killer cell mediated cytotoxicity / Transcriptional Regulation by VENTX / TAP binding / protein monoubiquitination / 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 / ubiquitin ligase complex / protein K48-linked ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / secretory granule membrane / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / Assembly of the pre-replicative complex / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / defense response / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / CDK-mediated phosphorylation and removal of Cdc6 / ISG15 antiviral mechanism / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / protein polyubiquitination / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / ubiquitin-protein transferase activity / Separation of Sister Chromatids / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / Antigen processing: Ubiquitination & Proteasome degradation / late endosome membrane / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / Senescence-Associated Secretory Phenotype (SASP) / early endosome membrane / amyloid fibril formation / ubiquitin-dependent protein catabolic process / protein homotetramerization
Similarity search - Function
Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / 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 / HLA class I histocompatibility antigen, B alpha chain / Ubiquitin-conjugating enzyme E2 E1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.788 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: Derived calculations / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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-15 alpha chain
B: Beta-2-microglobulin
C: Ubiquitin-conjugating enzyme E2 E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9537
Polymers44,6083
Non-polymers3444
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-47 kcal/mol
Surface area18540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.359, 81.389, 109.969
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


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 Ubiquitin-conjugating enzyme E2 E1 / Ubiquitin-protein ligase E1 / Ubiquitin carrier protein E1 / UbcH6


Mass: 902.046 Da / Num. of mol.: 1 / Fragment: residues 83-91 / Source method: obtained synthetically / Details: CHEMICAL SYNTHESIS / References: UniProt: P51965, ubiquitin-protein ligase

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Non-polymers , 4 types, 599 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M NH4Ac, 0.1M tri-Sodium Citrate dihydrate, pH 5.6, 30% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8414 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 20, 2004
RadiationMonochromator: Bent Single-Crystal Germanium Triangular Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8414 Å / Relative weight: 1
ReflectionResolution: 1.776→31.654 Å / Num. obs: 43204 / % possible obs: 97.44 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.068 / Net I/σ(I): 14.2
Reflection shellResolution: 1.78→1.87 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.5 / Num. measured all: 19646 / Num. unique all: 19646 / Rsym value: 0.298 / % possible all: 83.32

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: B*1501/LEKARGSTY Complex without Peptide

Resolution: 1.788→19.083 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.224 / WRfactor Rwork: 0.172 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23151 2172 5.027 %RANDOM
Rwork0.17695 ---
all0.18 43303 --
obs0.17968 41032 94.756 %-
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 20.306 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.788→19.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3147 0 20 595 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213422
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9284667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73223.224183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85515545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4081533
X-RAY DIFFRACTIONr_chiral_restr0.1030.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022744
X-RAY DIFFRACTIONr_nbd_refined0.1940.21640
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22267
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2527
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.247
X-RAY DIFFRACTIONr_mcbond_it0.9731.52081
X-RAY DIFFRACTIONr_mcangle_it1.49823291
X-RAY DIFFRACTIONr_scbond_it2.35431554
X-RAY DIFFRACTIONr_scangle_it3.7494.51376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.788-1.8340.2681530.2262786315093.302
1.834-1.8840.2481460.2022896306399.314
1.884-1.9380.2331320.1932842300399.034
1.938-1.9970.2551410.1832769291699.794
1.997-2.0620.2521460.1752619277699.604
2.062-2.1330.2711350.182611275399.746
2.133-2.2130.2211370.1792500264399.773
2.213-2.3020.2171400.1762392253699.842
2.302-2.4020.2721280.1823392467100
2.402-2.5180.241260.18222202346100
2.518-2.6510.2481100.17921292239100
2.651-2.8090.267950.18720232118100
2.809-2.9980.227960.17818931989100
2.998-3.2320.1881010.17617811882100
3.232-3.530.221950.16216401735100
3.53-3.930.212890.15515021591100
3.93-4.5060.215600.14513571417100
4.506-5.4430.212520.15711741226100
5.443-7.4030.255540.214943997100
7.403-19.0830.195360.21361665399.847

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