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- PDB-4jqx: HLA-B*44:03 in complex with Epstein-Barr virus BZLF1-derived pept... -

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Basic information

Entry
Database: PDB / ID: 4jqx
TitleHLA-B*44:03 in complex with Epstein-Barr virus BZLF1-derived peptide (residues 169-180)
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-44 alpha chain
  • Trans-activator protein BZLF1Transcription factor
KeywordsIMMUNE SYSTEM / immunoglobulin fold / antigen presentation / t-cell receptor / extracellular
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / 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 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / DNA-binding transcription factor activity / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain superfamily / Basic-leucine zipper domain / 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 / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Lytic switch protein BZLF1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTheodossis, A. / Welland, A. / Gras, S. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2013
Title: HLA Peptide Length Preferences Control CD8+ T Cell Responses.
Authors: Rist, M.J. / Theodossis, A. / Croft, N.P. / Neller, M.A. / Welland, A. / Chen, Z. / Sullivan, L.C. / Burrows, J.M. / Miles, J.J. / Brennan, R.M. / Gras, S. / Khanna, R. / Brooks, A.G. / ...Authors: Rist, M.J. / Theodossis, A. / Croft, N.P. / Neller, M.A. / Welland, A. / Chen, Z. / Sullivan, L.C. / Burrows, J.M. / Miles, J.J. / Brennan, R.M. / Gras, S. / Khanna, R. / Brooks, A.G. / McCluskey, J. / Purcell, A.W. / Rossjohn, J. / Burrows, S.R.
History
DepositionMar 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Sep 20, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-44 alpha chain
C: Beta-2-microglobulin
B: Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6266
Polymers45,4163
Non-polymers2103
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-20 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.816, 81.619, 110.336
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 AC

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


Mass: 32152.484 Da / Num. of mol.: 1 / Fragment: extracellular domains (UNP residues 25-302)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Production host: Escherichia coli (E. coli) / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: mature protein (UNP residues 21-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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Protein/peptide , 1 types, 1 molecules B

#3: Protein/peptide Trans-activator protein BZLF1 / Transcription factor / EB1 / Zebra


Mass: 1515.642 Da / Num. of mol.: 1 / Fragment: UNP residues 169-180 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KSS8

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Non-polymers , 3 types, 204 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsD156L (UNP D180L) IS A NATURAL VARIANT.

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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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M citrate, pH 5.6, 0.2 M ammonium acetate, 16-26% PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95668 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 6, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95668 Å / Relative weight: 1
ReflectionResolution: 1.9→40.18 Å / Num. all: 35075 / Num. obs: 35075 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.147 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5142 / % possible all: 97.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SYS

1sys


Resolution: 1.9→38.275 Å / SU ML: 0.24 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2311 1751 5 %RANDOM
Rwork0.1946 ---
obs0.1965 35037 94.9 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.837 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2186 Å2-0 Å20 Å2
2---4.2005 Å2-0 Å2
3---4.4191 Å2
Refinement stepCycle: LAST / Resolution: 1.9→38.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 14 201 3403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073300
X-RAY DIFFRACTIONf_angle_d1.0524476
X-RAY DIFFRACTIONf_dihedral_angle_d12.9811238
X-RAY DIFFRACTIONf_chiral_restr0.077462
X-RAY DIFFRACTIONf_plane_restr0.004591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.95140.27021370.25242548X-RAY DIFFRACTION96
1.9514-2.00880.25571400.21832585X-RAY DIFFRACTION98
2.0088-2.07370.26661370.21242585X-RAY DIFFRACTION98
2.0737-2.14780.23611230.20662651X-RAY DIFFRACTION99
2.1478-2.23380.24841480.19322622X-RAY DIFFRACTION99
2.2338-2.33540.23031420.19072667X-RAY DIFFRACTION99
2.3354-2.45850.22281390.19912626X-RAY DIFFRACTION99
2.4585-2.61250.25041400.18992648X-RAY DIFFRACTION99
2.6125-2.81420.24031340.19272650X-RAY DIFFRACTION98
2.8142-3.09730.22961380.18222616X-RAY DIFFRACTION97
3.0973-3.54520.20871210.17172639X-RAY DIFFRACTION96
3.5452-4.46540.2171090.16592026X-RAY DIFFRACTION74
4.4654-38.28320.21291430.22312423X-RAY DIFFRACTION84

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