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- PDB-3sjv: Crystal structure of the RL42 TCR in complex with HLA-B8-FLR -

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Basic information

Entry
Database: PDB / ID: 3sjv
TitleCrystal structure of the RL42 TCR in complex with HLA-B8-FLR
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Epstein-Barr nuclear antigen 3
  • HLA class I histocompatibility antigen, B-8 alpha chain
  • RL42 T cell receptor, alpha chain
  • RL42 T cell receptor, beta chain
KeywordsIMMUNE SYSTEM / T cell
Function / homology
Function and homology information


host cell nuclear matrix / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules ...host cell nuclear matrix / alpha-beta T cell receptor complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / PD-1 signaling / 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 / viral process / secretory granule membrane / 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 / 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 / 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 / Interferon alpha/beta signaling / 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-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 / Amyloid fiber formation / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
Similarity search - Function
Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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 ...Epstein-Barr virus nuclear antigen 3/4/6 / Epstein-Barr virus nuclear antigen 3 (EBNA-3) / T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / 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
T cell receptor alpha chain constant / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / Epstein-Barr nuclear antigen 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Human herpesvirus 4 (Epstein-Barr virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsGras, S. / Wilmann, P.G. / Zhenjun, C. / Hanim, H. / Yu Chih, L. / Kjer-Nielsen, L. / Purcell, A.W. / Burrows, S.R. / Mccluskey, J. / Rossjohn, J.
CitationJournal: J.Immunol. / Year: 2012
Title: A structural basis for varied alpha-beta TCR usage against an immunodominant EBV antigen restricted to a HLA-B8 molecule.
Authors: Gras, S. / Wilmann, P.G. / Chen, Z. / Halim, H. / Liu, Y.C. / Kjer-Nielsen, L. / Purcell, A.W. / Burrows, S.R. / McCluskey, J. / Rossjohn, J.
History
DepositionJun 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Structure summary
Revision 1.2Feb 5, 2020Group: Advisory / Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 3
D: RL42 T cell receptor, alpha chain
E: RL42 T cell receptor, beta chain
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: Epstein-Barr nuclear antigen 3
I: RL42 T cell receptor, alpha chain
J: RL42 T cell receptor, beta chain
K: HLA class I histocompatibility antigen, B-8 alpha chain
L: Beta-2-microglobulin
M: Epstein-Barr nuclear antigen 3
N: RL42 T cell receptor, alpha chain
O: RL42 T cell receptor, beta chain
P: HLA class I histocompatibility antigen, B-8 alpha chain
Q: Beta-2-microglobulin
R: Epstein-Barr nuclear antigen 3
S: RL42 T cell receptor, alpha chain
T: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)380,39020
Polymers380,39020
Non-polymers00
Water0
1
A: HLA class I histocompatibility antigen, B-8 alpha chain
B: Beta-2-microglobulin
C: Epstein-Barr nuclear antigen 3
D: RL42 T cell receptor, alpha chain
E: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers95,0975
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA class I histocompatibility antigen, B-8 alpha chain
G: Beta-2-microglobulin
H: Epstein-Barr nuclear antigen 3
I: RL42 T cell receptor, alpha chain
J: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers95,0975
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: HLA class I histocompatibility antigen, B-8 alpha chain
L: Beta-2-microglobulin
M: Epstein-Barr nuclear antigen 3
N: RL42 T cell receptor, alpha chain
O: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers95,0975
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: HLA class I histocompatibility antigen, B-8 alpha chain
Q: Beta-2-microglobulin
R: Epstein-Barr nuclear antigen 3
S: RL42 T cell receptor, alpha chain
T: RL42 T cell receptor, beta chain


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers95,0975
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.080, 185.000, 217.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein
HLA class I histocompatibility antigen, B-8 alpha chain / MHC class I antigen B*8


Mass: 32015.055 Da / Num. of mol.: 4 / Fragment: Extracellular domain residues 25-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30460, UniProt: P01889*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 4
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
#3: Protein/peptide
Epstein-Barr nuclear antigen 3 / EBNA-3 / EBV nuclear antigen 3 / Epstein-Barr nuclear antigen 3A / EBNA-3A / EBV nuclear antigen 3A


Mass: 1054.247 Da / Num. of mol.: 4 / Fragment: sequence database residues 325-333 / Source method: obtained synthetically / Source: (synth.) Human herpesvirus 4 (Epstein-Barr virus) / References: UniProt: Q3KST2
#4: Protein
RL42 T cell receptor, alpha chain


Mass: 22686.078 Da / Num. of mol.: 4
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
RL42 T cell receptor, beta chain


Mass: 27462.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): bl21

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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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M ammonium tartrate, 14% PEG 3350, 7% ethylene glycol, pH 8, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 3.1→100 Å / Num. obs: 73724 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.401 Å2 / Rmerge(I) obs: 0.118 / Net I/σ(I): 14.85
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
3.1-3.20.7073.15498216625199.9
3.2-3.30.5514.03439095847199.9
3.3-3.40.4335391395215199.9
3.4-3.50.3326.453453746091100
3.5-3.60.2618.023084541241100
3.6-3.70.2229.192783537351100
3.7-3.80.18710.592469932971100
3.8-3.90.16811.722239429961100
3.9-40.14313.192021427141100
4-50.08919.64124224167911100
5-60.07722.165462074791100
6-100.05128.945814982231100
10-1000.03242.47140852069185.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KGC, 1M05

1kgc

1m05


Resolution: 3.1→19.991 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7281 / SU ML: 0.51 / σ(F): 0.01 / Phase error: 33.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3213 3385 5.06 %
Rwork0.2527 --
obs0.2562 66875 90.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 13.192 Å2 / ksol: 0.202 e/Å3
Displacement parametersBiso max: 256.49 Å2 / Biso mean: 86.5767 Å2 / Biso min: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.1368 Å2-0 Å20 Å2
2---6.3521 Å2-0 Å2
3---9.4889 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26455 0 0 0 26455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00327162
X-RAY DIFFRACTIONf_angle_d0.68536837
X-RAY DIFFRACTIONf_chiral_restr0.0493841
X-RAY DIFFRACTIONf_plane_restr0.0034885
X-RAY DIFFRACTIONf_dihedral_angle_d13.3299971
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.21040.39912750.35275181545675
3.2104-3.33840.41052810.32715542582380
3.3384-3.48950.37033160.30375834615085
3.4895-3.67240.35223720.28816158653089
3.6724-3.90090.34243420.25926359670191
3.9009-4.19960.29423420.23626621696395
4.1996-4.61750.29543510.21826765711697
4.6175-5.27490.27233630.21216894725798
5.2749-6.60570.32793520.23646937728998
6.6057-19.9910.28813910.22687199759099

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