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- PDB-4jqv: HLA-B*18:01 in complex with Epstein-Barr virus BZLF1-derived pept... -

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Basic information

Entry
Database: PDB / ID: 4jqv
TitleHLA-B*18:01 in complex with Epstein-Barr virus BZLF1-derived peptide (residues 173-180)
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, B-18 alpha chain
  • Trans-activator protein BZLF1
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 / symbiont-mediated perturbation of host cell cycle progression / 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 ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle progression / 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 / DNA-binding transcription factor activity / Golgi membrane / external side of plasma membrane / signaling receptor binding / lysosomal membrane / innate immune response / focal adhesion / Neutrophil degranulation / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / Basic-leucine zipper (bZIP) domain signature. / Basic-leucine zipper domain / Basic-leucine zipper domain superfamily / 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 / Basic-leucine zipper domain superfamily / 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
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: 1.5 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
Revision 1.3Nov 20, 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-18 alpha chain
C: Beta-2-microglobulin
B: Trans-activator protein BZLF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7684
Polymers44,7093
Non-polymers591
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-17 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.848, 81.251, 110.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class I histocompatibility antigen, B-18 alpha chain / MHC class I antigen B*18


Mass: 31922.047 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: P30466, UniProt: P01889*PLUS
#2: Protein 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
#3: Protein/peptide Trans-activator protein BZLF1 / EB1 / Zebra


Mass: 1039.183 Da / Num. of mol.: 1 / Fragment: UNP residues 173-180 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KSS8
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 51.99 %
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: APS / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→46.22 Å / Num. all: 73568 / Num. obs: 73568 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 12.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.4 / Num. unique all: 10522 / % possible all: 98.5

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Processing

Software
NameVersionClassification
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: 1.5→40.626 Å / SU ML: 0.2 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2142 3713 5.05 %RANDOM
Rwork0.1894 ---
obs0.1907 73505 98.94 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.252 Å2 / ksol: 0.398 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.8621 Å20 Å20 Å2
2---1.4667 Å2-0 Å2
3---3.3288 Å2
Refinement stepCycle: LAST / Resolution: 1.5→40.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3141 0 4 422 3567
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063286
X-RAY DIFFRACTIONf_angle_d1.0674469
X-RAY DIFFRACTIONf_dihedral_angle_d12.6671241
X-RAY DIFFRACTIONf_chiral_restr0.077459
X-RAY DIFFRACTIONf_plane_restr0.005592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5190.31291180.29182567X-RAY DIFFRACTION99
1.519-1.5390.29611330.27652483X-RAY DIFFRACTION97
1.539-1.56010.27731360.26332552X-RAY DIFFRACTION100
1.5601-1.58230.28811360.23542538X-RAY DIFFRACTION98
1.5823-1.6060.24341370.22722545X-RAY DIFFRACTION99
1.606-1.63110.25071460.22382534X-RAY DIFFRACTION98
1.6311-1.65780.24511370.22152542X-RAY DIFFRACTION99
1.6578-1.68640.25951370.2132541X-RAY DIFFRACTION99
1.6864-1.71710.23611240.20772571X-RAY DIFFRACTION99
1.7171-1.75010.25941250.19652559X-RAY DIFFRACTION98
1.7501-1.78580.20991530.19322556X-RAY DIFFRACTION99
1.7858-1.82460.21441400.192531X-RAY DIFFRACTION98
1.8246-1.86710.26311340.19452579X-RAY DIFFRACTION100
1.8671-1.91380.23291390.18792579X-RAY DIFFRACTION99
1.9138-1.96550.22651290.18062594X-RAY DIFFRACTION99
1.9655-2.02340.22481470.18352566X-RAY DIFFRACTION100
2.0234-2.08870.19341140.18312608X-RAY DIFFRACTION99
2.0887-2.16330.20511450.18112574X-RAY DIFFRACTION99
2.1633-2.24990.19911530.18142584X-RAY DIFFRACTION99
2.2499-2.35230.19321510.17792579X-RAY DIFFRACTION99
2.3523-2.47630.21921520.19532597X-RAY DIFFRACTION99
2.4763-2.63140.21731280.18852630X-RAY DIFFRACTION99
2.6314-2.83460.19881330.19672636X-RAY DIFFRACTION99
2.8346-3.11970.19381330.18482640X-RAY DIFFRACTION99
3.1197-3.57090.18631340.17212653X-RAY DIFFRACTION99
3.5709-4.4980.16131300.15312676X-RAY DIFFRACTION99
4.498-40.64050.24891690.20282778X-RAY DIFFRACTION99

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