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- PDB-3dx8: Crystal Structure of B*4405 presenting a 10mer EBV epitope -

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Basic information

Entry
Database: PDB / ID: 3dx8
TitleCrystal Structure of B*4405 presenting a 10mer EBV epitope
Components
  • Beta-2-microglobulin
  • EBV decapeptide epitope
  • HLA class I histocompatibility complex HLA-B*4405
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 / lumenal side of endoplasmic reticulum membrane / 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 / defense response / 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 / 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 / Interferon alpha/beta signaling / 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 / protein-folding chaperone binding / 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 / lysosomal membrane / external side of plasma membrane / Golgi 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 / MHC class I-like antigen recognition-like ...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
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: 2.1 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 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 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*4405
B: Beta-2-microglobulin
C: EBV decapeptide epitope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2435
Polymers45,0593
Non-polymers1842
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4770 Å2
ΔGint-17 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.776, 82.351, 110.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility complex HLA-B*4405 / HLA class I histocompatibility antigen / B-44 alpha chain / MHC class I antigen B*44 / Bw-44


Mass: 32028.348 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
#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
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.56 Å3/Da / Density % sol: 51.86 %
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: Apr 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→65.94 Å / Num. all: 26691 / Num. obs: 26691

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→65.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.628 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.233 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1344 5.1 %RANDOM
Rwork0.193 ---
all0.197 26691 --
obs0.197 26568 95.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.29 Å2 / Biso mean: 29.388 Å2 / Biso min: 3.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2---1.19 Å20 Å2
3---1.97 Å2
Refinement stepCycle: LAST / Resolution: 2.1→65.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3178 0 12 223 3413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213366
X-RAY DIFFRACTIONr_bond_other_d0.0010.022372
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9424580
X-RAY DIFFRACTIONr_angle_other_deg0.9073.0025689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5075402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.69822.926188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76115561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0841538
X-RAY DIFFRACTIONr_chiral_restr0.1020.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02753
X-RAY DIFFRACTIONr_nbd_refined0.1880.2527
X-RAY DIFFRACTIONr_nbd_other0.1960.22473
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21543
X-RAY DIFFRACTIONr_nbtor_other0.0820.21858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2200
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0890.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2240.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.214
X-RAY DIFFRACTIONr_mcbond_it2.13932566
X-RAY DIFFRACTIONr_mcbond_other0.383781
X-RAY DIFFRACTIONr_mcangle_it2.62453197
X-RAY DIFFRACTIONr_scbond_it3.89471666
X-RAY DIFFRACTIONr_scangle_it4.959101377
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 93 -
Rwork0.216 1792 -
all-1885 -
obs--92.86 %

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