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- PDB-3kpr: Crystal Structure of the LC13 TCR in complex with HLA B*4405 boun... -

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Basic information

Entry
Database: PDB / ID: 3kpr
TitleCrystal Structure of the LC13 TCR in complex with HLA B*4405 bound to EEYLKAWTF a mimotope
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • EEYLKAWTF, mimotope peptide
  • HLA class I histocompatibility antigen, B-44 alpha chain
  • LC13 TCR alpha chain
  • LC13 TCR beta chain
KeywordsIMMUNE SYSTEM / HLA B*4405 / TCRpMHC structure / ternary complex / allorecognition / TCR recognition / self peptide / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Polymorphism
Function / homology
Function and homology information


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 / TAP binding ...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 / TAP binding / PD-1 signaling / protection from natural killer cell mediated cytotoxicity / immunoglobulin complex, circulating / immunoglobulin receptor binding / detection of bacterium / complement activation, classical pathway / 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / antigen binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / 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 / defense response / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / Downstream TCR signaling / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / blood microparticle / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses
Similarity search - Function
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 ...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 / T cell receptor beta constant 1 / HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMacdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. ...Macdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. / Crawford, F. / Stadinsky, B. / Jackson, D. / Brooks, A.G. / Purcell, A.W. / Kappler, J.W. / Burrows, S.R. / Rossjohn, J. / McCluskey, J.
CitationJournal: Immunity / Year: 2009
Title: T cell allorecognition via molecular mimicry.
Authors: Macdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. / Crawford, F. / Stadinsky, B. / ...Authors: Macdonald, W.A. / Chen, Z. / Gras, S. / Archbold, J.K. / Tynan, F.E. / Clements, C.S. / Bharadwaj, M. / Kjer-Nielsen, L. / Saunders, P.M. / Wilce, M.C. / Crawford, F. / Stadinsky, B. / Jackson, D. / Brooks, A.G. / Purcell, A.W. / Kappler, J.W. / Burrows, S.R. / Rossjohn, J. / McCluskey, J.
History
DepositionNov 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-44 alpha chain
B: Beta-2-microglobulin
C: EEYLKAWTF, mimotope peptide
D: LC13 TCR alpha chain
E: LC13 TCR beta chain
F: HLA class I histocompatibility antigen, B-44 alpha chain
G: Beta-2-microglobulin
H: EEYLKAWTF, mimotope peptide
I: LC13 TCR alpha chain
J: LC13 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)188,86910
Polymers188,86910
Non-polymers00
Water2,090116
1
A: HLA class I histocompatibility antigen, B-44 alpha chain
B: Beta-2-microglobulin
C: EEYLKAWTF, mimotope peptide
D: LC13 TCR alpha chain
E: LC13 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4355
Polymers94,4355
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-44 kcal/mol
Surface area38550 Å2
MethodPISA
2
F: HLA class I histocompatibility antigen, B-44 alpha chain
G: Beta-2-microglobulin
H: EEYLKAWTF, mimotope peptide
I: LC13 TCR alpha chain
J: LC13 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4355
Polymers94,4355
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11270 Å2
ΔGint-42 kcal/mol
Surface area38310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)223.117, 53.217, 143.202
Angle α, β, γ (deg.)90.000, 102.390, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

#1: Protein HLA class I histocompatibility antigen, B-44 alpha chain / MHC class I antigen B*44 / Bw-44


Mass: 32028.348 Da / Num. of mol.: 2 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P30481, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11748.160 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61769
#4: Protein LC13 TCR alpha chain


Mass: 22317.717 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01848*PLUS
#5: Protein LC13 TCR beta chain


Mass: 27153.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01850*PLUS

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Protein/peptide / Non-polymers , 2 types, 118 molecules CH

#3: Protein/peptide EEYLKAWTF, mimotope peptide


Mass: 1187.319 Da / Num. of mol.: 2 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M NaOAc, 12-18% PEG 4000, 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 50197 / % possible obs: 97.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.112 / Χ2: 1.262 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.6930.45349760.96797.8
2.69-2.83.30.36951060.90199.8
2.8-2.933.30.28550650.979100
2.93-3.083.40.21250471.05199.9
3.08-3.283.30.16951241.19199.8
3.28-3.533.20.13150201.41798.5
3.53-3.882.90.09848721.50395.3
3.88-4.453.10.07349641.75196.1
4.45-5.63.10.06147761.74992.5
5.6-503.20.04352471.26998.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1SYV and 1KGC

1syv

1kgc


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.864 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.768 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 2538 5.1 %RANDOM
Rwork0.219 ---
obs0.222 50191 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 64.18 Å2 / Biso mean: 36.4 Å2 / Biso min: 15.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å21.74 Å2
2---1.7 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13318 0 0 116 13434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02113680
X-RAY DIFFRACTIONr_angle_refined_deg0.9261.93818614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7551642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6123.859710
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.009152196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.08415104
X-RAY DIFFRACTIONr_chiral_restr0.0620.21960
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0210752
X-RAY DIFFRACTIONr_nbd_refined0.1680.25286
X-RAY DIFFRACTIONr_nbtor_refined0.2950.29056
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2536
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.218
X-RAY DIFFRACTIONr_mcbond_it0.59138532
X-RAY DIFFRACTIONr_mcangle_it1.033513384
X-RAY DIFFRACTIONr_scbond_it1.51675987
X-RAY DIFFRACTIONr_scangle_it2.366105230
LS refinement shellResolution: 2.6→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 207 -
Rwork0.29 3390 -
all-3597 -
obs--94.73 %

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