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- PDB-4jry: Crystal Structure of SB47 TCR-HLA B*3505-LPEP complex -

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Basic information

Entry
Database: PDB / ID: 4jry
TitleCrystal Structure of SB47 TCR-HLA B*3505-LPEP complex
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • SB47 TCR alpha chain
  • SB47 TCR beta chain
  • Trans-activator protein BZLF1
KeywordsIMMUNE SYSTEM / TCR / T cell / HLA B*3508 / LPEP / EBV / alloreactivity
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 / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of peptide antigen via MHC class I / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / : ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / symbiont-mediated perturbation of host cell cycle progression / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / antigen processing and presentation of peptide antigen via MHC class I / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / : / : / 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 / response to bacterium / 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 / 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 / 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 / Downstream TCR signaling / T cell receptor signaling pathway / 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 / lysosomal membrane / 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 / plasma membrane / cytosol
Similarity search - Function
Trans-activator protein BZLF1, human herpesvirus 4 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...Trans-activator protein BZLF1, human herpesvirus 4 / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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
HLA-B*3507 / T cell receptor alpha chain constant / T cell receptor beta constant 1 / 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 / molecular replacement / Resolution: 2.8 Å
AuthorsLiu, Y.C. / Rossjohn, J. / Gras, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Highly divergent T-cell receptor binding modes underlie specific recognition of a bulged viral peptide bound to a human leukocyte antigen class I molecule.
Authors: Liu, Y.C. / Miles, J.J. / Neller, M.A. / Gostick, E. / Price, D.A. / Purcell, A.W. / McCluskey, J. / Burrows, S.R. / Rossjohn, J. / Gras, S.
History
DepositionMar 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: MHC class I antigen
B: Beta-2-microglobulin
C: Trans-activator protein BZLF1
D: SB47 TCR alpha chain
E: SB47 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1798
Polymers95,1085
Non-polymers723
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-81 kcal/mol
Surface area38010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)237.600, 237.600, 61.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen / heavy chain HLA B*3508


Mass: 31984.281 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C5MK56
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein SB47 TCR alpha chain


Mass: 22433.096 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#5: Protein SB47 TCR beta chain


Mass: 27384.186 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS

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Protein/peptide , 1 types, 1 molecules C

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


Mass: 1426.612 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 52-64 / Source method: obtained synthetically / Details: commercial source / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KSS8

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Non-polymers , 3 types, 127 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 72.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 10K, 0.2M Na tartrate, 10mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.8→168 Å / Num. obs: 42851 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 46.502 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 9.59
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.8-2.90.3040.4763.4531899420842080.511100
2.9-30.2190.374.5327708366736670.398100
3-50.0960.169.7418826527052270330.17499.9
5-60.0530.10713.9320936319131890.11699.9
6-100.0450.09315.1524066347334730.1100
100.0320.06916.856829102010110.07599.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Iceicedata collection
XDSdata reduction
BUSTERrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AK4, 1ZHK

2ak4

1zhk


Resolution: 2.8→100 Å / Occupancy max: 1 / Occupancy min: 0
RfactorNum. reflection
Rfree0.233 2142
Rwork0.2 -
obs-42581
Displacement parametersBiso max: 139 Å2 / Biso mean: 46.3105 Å2 / Biso min: 7.4 Å2
Refinement stepCycle: LAST / Resolution: 2.8→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6703 0 3 124 6830
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONTORSION ANGLES2343SINUSOIDAL2
X-RAY DIFFRACTIONTRIGONAL CARBON PLANES193HARMONIC2
X-RAY DIFFRACTIONGENERAL PLANES995HARMONIC5
X-RAY DIFFRACTIONISOTROPIC THERMAL FACTORS6880HARMONIC20
X-RAY DIFFRACTIONBAD NON-BONDED CONTACTS0SEMIHARMONIC5
X-RAY DIFFRACTIONIMPROPER TORSIONS
X-RAY DIFFRACTIONPSEUDOROTATION ANGLES
X-RAY DIFFRACTIONCHIRAL IMPROPER TORSION866SEMIHARMONIC5
X-RAY DIFFRACTIONSUM OF OCCUPANCIES
X-RAY DIFFRACTIONUTILITY DISTANCES
X-RAY DIFFRACTIONUTILITY ANGLES
X-RAY DIFFRACTIONUTILITY TORSION
X-RAY DIFFRACTIONIDEAL-DIST CONTACT TERM7795SEMIHARMONIC4
X-RAY DIFFRACTIONBOND LENGTHS (A)6880HARMONIC20.012
X-RAY DIFFRACTIONBOND ANGLES (DEGREES)9351HARMONIC21.21
X-RAY DIFFRACTIONPEPTIDE OMEGA TORSION ANGLES (DEGREES)3.79
X-RAY DIFFRACTIONOTHER TORSION ANGLES (DEGREES)22.78

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