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- PDB-3dx7: Crystal Structure of HLA-B*4403 presenting 10mer EBV antigen -

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Basic information

Entry
Database: PDB / ID: 3dx7
TitleCrystal Structure of HLA-B*4403 presenting 10mer EBV antigen
Components
  • Beta-2-microglobulin
  • EBV decapeptide epitope
  • HLA class I histocompatibility complex HLA-B*4403
KeywordsIMMUNE SYSTEM / MHC / Glycoprotein / Glycation / Host-virus interaction / Immune response / Membrane / MHC I / Transmembrane / Pyrrolidone carboxylic acid / Disease mutation
Function / homology
Function and homology information


host cell nuclear matrix / viral latency / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium ...host cell nuclear matrix / viral latency / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / secretory granule membrane / 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 / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / 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 / defense response / 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 / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / HLA class I histocompatibility antigen, B alpha chain / Epstein-Barr nuclear antigen 6 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsArchbold, J.K. / Ely, L.K. / Rossjohn, J.
CitationJournal: J.Exp.Med. / Year: 2009
Title: Natural micropolymorphism in human leukocyte antigens provides a basis for genetic control of antigen recognition.
Authors: Archbold, J.K. / Macdonald, W.A. / Gras, S. / Ely, L.K. / Miles, J.J. / Bell, M.J. / Brennan, R.M. / Beddoe, T. / Wilce, M.C. / Clements, C.S. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J.
History
DepositionJul 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility complex HLA-B*4403
B: Beta-2-microglobulin
C: EBV decapeptide epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4299
Polymers45,0093
Non-polymers4206
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-20 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.411, 81.791, 109.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 complex HLA-B*4403 / HLA class I histocompatibility antigen / B-44 alpha chain / MHC class I antigen B*44 / Bw-44


Mass: 31978.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide EBV decapeptide epitope


Mass: 1282.421 Da / Num. of mol.: 1 / Fragment: residues 281-290 / Source method: obtained synthetically
Details: sequence occurs in Human herpesvirus 4, gene EBNA6, BERF3-BERF4
References: UniProt: P03204

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Non-polymers , 3 types, 407 molecules

#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / 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: 2.5 Å3/Da / Density % sol: 50.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Citrate, Ammonium Acetate, PEG 4000, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→109.11 Å / Num. all: 59003 / Num. obs: 59003

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→109.11 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.663 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2977 5.1 %RANDOM
Rwork0.183 ---
all0.184 ---
obs0.184 58846 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.81 Å2 / Biso mean: 21.014 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.6→109.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 28 401 3604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213494
X-RAY DIFFRACTIONr_bond_other_d0.0010.022448
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.9484784
X-RAY DIFFRACTIONr_angle_other_deg0.8023.0025918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4435441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.21423.109193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.87915597
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1881538
X-RAY DIFFRACTIONr_chiral_restr0.0760.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023980
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02772
X-RAY DIFFRACTIONr_nbd_refined0.190.2606
X-RAY DIFFRACTIONr_nbd_other0.1920.22649
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21614
X-RAY DIFFRACTIONr_nbtor_other0.0810.21909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2306
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2470.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.223
X-RAY DIFFRACTIONr_mcbond_it1.38832695
X-RAY DIFFRACTIONr_mcbond_other0.2663801
X-RAY DIFFRACTIONr_mcangle_it1.6853335
X-RAY DIFFRACTIONr_scbond_it2.42371725
X-RAY DIFFRACTIONr_scangle_it3.165101421
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 186 -
Rwork0.239 3460 -
all-3646 -
obs--83.49 %

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