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- PDB-2nx5: Crystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV ... -

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Basic information

Entry
Database: PDB / ID: 2nx5
TitleCrystal structure of ELS4 TCR bound to HLA-B*3501 presenting EBV peptide EPLPQGQLTAY at 1.7A
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • EBV peptide, EPLPQGQLTAY
  • ELS4 TCR alpha chain
  • ELS4 TCR beta chain
  • HLA-B35
KeywordsIMMUNE SYSTEM / TCR-pMHC / immune complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / 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 ...symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / release from viral latency / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / 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 / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / 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 / defense response / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / sequence-specific DNA binding / adaptive immune response / learning or memory / protein dimerization activity / immune response / Amyloid fiber formation / DNA-binding transcription factor activity / lysosomal membrane / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / host cell nucleus / chromatin
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
HLA-B35 / T cell receptor alpha chain constant / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, B alpha chain / Lytic switch protein BZLF1 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTynan, F.E. / Reid, H.H. / Rossjohn, J.
CitationJournal: Nat.Immunol. / Year: 2007
Title: A T cell receptor flattens a bulged antigenic peptide presented by a major histocompatibility complex class I molecule
Authors: Tynan, F.E. / Reid, H.H. / Kjer-Nielsen, L. / Miles, J.J. / Wilce, M.C. / Kostenko, L. / Borg, N.A. / Williamson, N.A. / Beddoe, T. / Purcell, A.W. / Burrows, S.R. / McCluskey, J. / Rossjohn, J.
History
DepositionNov 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-B35
B: Beta-2-microglobulin
C: EBV peptide, EPLPQGQLTAY
D: ELS4 TCR alpha chain
E: ELS4 TCR beta chain
F: HLA-B35
G: Beta-2-microglobulin
H: EBV peptide, EPLPQGQLTAY
I: ELS4 TCR alpha chain
J: ELS4 TCR beta chain
K: HLA-B35
L: Beta-2-microglobulin
M: EBV peptide, EPLPQGQLTAY
N: ELS4 TCR alpha chain
P: ELS4 TCR beta chain
Q: HLA-B35
R: Beta-2-microglobulin
S: EBV peptide, EPLPQGQLTAY
T: ELS4 TCR alpha chain
U: ELS4 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)372,98020
Polymers372,98020
Non-polymers00
Water3,495194
1
A: HLA-B35
B: Beta-2-microglobulin
C: EBV peptide, EPLPQGQLTAY
D: ELS4 TCR alpha chain
E: ELS4 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,2455
Polymers93,2455
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: HLA-B35
G: Beta-2-microglobulin
I: ELS4 TCR alpha chain
J: ELS4 TCR beta chain
M: EBV peptide, EPLPQGQLTAY


Theoretical massNumber of molelcules
Total (without water)93,2455
Polymers93,2455
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
H: EBV peptide, EPLPQGQLTAY
K: HLA-B35
L: Beta-2-microglobulin
N: ELS4 TCR alpha chain
P: ELS4 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,2455
Polymers93,2455
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
Q: HLA-B35
R: Beta-2-microglobulin
S: EBV peptide, EPLPQGQLTAY
T: ELS4 TCR alpha chain
U: ELS4 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)93,2455
Polymers93,2455
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.479, 118.067, 131.465
Angle α, β, γ (deg.)90.000, 96.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 16 molecules AFKQBGLRDINTEJPU

#1: Protein
HLA-B35 / HLA-B*3501 heavy chain


Mass: 31940.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B-3501 / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O19626, UniProt: P01889*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11748.160 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein
ELS4 TCR alpha chain / T-cell receptor / alpha chain


Mass: 20891.129 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#5: Protein
ELS4 TCR beta chain / T-cell receptor / beta chain


Mass: 27449.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS

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Protein/peptide / Non-polymers , 2 types, 198 molecules CHMS

#3: Protein/peptide
EBV peptide, EPLPQGQLTAY


Mass: 1216.339 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is derived from the Epstein Barr virus BZLF1 protein.
References: UniProt: P03206*PLUS
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.45 Å3/Da / Density % sol: 49.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M Na Cacodylate (pH6.4), 0.2M CaCl2, 16% PEG 3350, 3% 1,6Hexanediol, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID
DetectorDate: Nov 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionHighest resolution: 2.7 Å / Num. obs: 87783

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZSD, 2NW2

1zsd

2nw2


Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.797 / SU B: 18.556 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.505 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32702 4598 5 %RANDOM
Rwork0.26876 ---
obs0.27169 87783 93.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.267 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20.17 Å2
2--1.64 Å20 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26287 0 0 194 26481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02127011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9591.93436727
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.24653248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78823.8351408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.581154315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.89515200
X-RAY DIFFRACTIONr_chiral_restr0.0660.23836
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0221268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.210912
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.217606
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2929
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.829316794
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5526344
X-RAY DIFFRACTIONr_scbond_it1.806711852
X-RAY DIFFRACTIONr_scangle_it2.7311010383
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.701→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 353 -
Rwork0.393 6562 -
obs--96.5 %

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