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- PDB-4jrx: Crystal Structure of CA5 TCR-HLA B*3505-LPEP complex -

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Basic information

Entry
Database: PDB / ID: 4jrx
TitleCrystal Structure of CA5 TCR-HLA B*3505-LPEP complex
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • CA5 TCR alpha chain
  • CA5 TCR beta chain
  • MHC class I antigen
  • Trans-activator protein BZLF1Transcription factor
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 / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / antigen processing and presentation / PD-1 signaling / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / alpha-beta T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / antigen processing and presentation / PD-1 signaling / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / response to bacterium / 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 / 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 / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / adaptive immune response / learning or memory / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / focal adhesion / 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 / 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 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 ...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 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
IODIDE ION / 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: 2.3 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: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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: MHC class I antigen
B: Beta-2-microglobulin
C: Trans-activator protein BZLF1
D: CA5 TCR alpha chain
E: CA5 TCR beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,35216
Polymers95,2675
Non-polymers1,08411
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.100, 78.408, 105.339
Angle α, β, γ (deg.)90.000, 93.060, 90.000
Int Tables number4
Space group name H-MP1211

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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 / 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: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein CA5 TCR alpha chain


Mass: 23264.641 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 CA5 TCR beta chain


Mass: 26843.803 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 / Transcription factor / 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, 143 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: I
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.39 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 16% PEG 3350, 0.2M KI, 0.1M Na-cacodylate pH 6.7, 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: Mar 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 2.3→19.8 Å / Num. obs: 39947 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.999 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 13.2
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
2.3-2.50.4250.5053.9856298877087700.548100
2.5-30.1790.228.118369613056130540.239100
3-40.0520.08518.436609510408104080.092100
4-60.0320.06524.7933398539553920.07199.9
6-100.030.06326.2211241179217920.068100
100.0280.06328.427595274570.06886.7

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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: 2.3→19.8 Å / Occupancy max: 1 / Occupancy min: 0.5
RfactorNum. reflection
Rfree0.257 1997
Rwork0.205 -
obs-39873
Displacement parametersBiso max: 128.27 Å2 / Biso mean: 39.7731 Å2 / Biso min: 8.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6714 0 11 132 6857
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONTORSION ANGLES2351SINUSOIDAL2
X-RAY DIFFRACTIONTRIGONAL CARBON PLANES198HARMONIC2
X-RAY DIFFRACTIONGENERAL PLANES996HARMONIC5
X-RAY DIFFRACTIONISOTROPIC THERMAL FACTORS6900HARMONIC20
X-RAY DIFFRACTIONBAD NON-BONDED CONTACTS1SEMIHARMONIC5
X-RAY DIFFRACTIONIMPROPER TORSIONS
X-RAY DIFFRACTIONPSEUDOROTATION ANGLES
X-RAY DIFFRACTIONCHIRAL IMPROPER TORSION875SEMIHARMONIC5
X-RAY DIFFRACTIONSUM OF OCCUPANCIES
X-RAY DIFFRACTIONUTILITY DISTANCES
X-RAY DIFFRACTIONUTILITY ANGLES
X-RAY DIFFRACTIONUTILITY TORSION
X-RAY DIFFRACTIONIDEAL-DIST CONTACT TERM7465SEMIHARMONIC4
X-RAY DIFFRACTIONBOND LENGTHS (A)6900HARMONIC20.008
X-RAY DIFFRACTIONBOND ANGLES (DEGREES)9381HARMONIC21.08
X-RAY DIFFRACTIONPEPTIDE OMEGA TORSION ANGLES (DEGREES)3.23
X-RAY DIFFRACTIONOTHER TORSION ANGLES (DEGREES)21.68

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