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

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Basic information

Entry
Database: PDB / ID: 3kps
TitleCrystal Structure of the LC13 TCR in complex with HLA B*4405 bound to EEYLQAFTY a self peptide from the ABCD3 protein
Components
  • Beta-2-microglobulin
  • EEYLQAFTY, self peptide from the ATP binding cassette protein ABCD3
  • 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


regulation of interleukin-12 production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity ...regulation of interleukin-12 production / regulation of dendritic cell differentiation / alpha-beta T cell receptor complex / regulation of T cell anergy / regulation of interleukin-6 production / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / TAP binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / Generation of second messenger molecules / Co-inhibition by PD-1 / 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 / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / response to bacterium / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / defense response / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / Downstream TCR signaling / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / negative regulation of neuron projection development / protein-folding chaperone binding / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / adaptive immune response / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane
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 ...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 / Immunoglobulin-like fold / Immunoglobulins / 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: 2.7 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
Revision 1.4Oct 9, 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: HLA class I histocompatibility antigen, B-44 alpha chain
B: Beta-2-microglobulin
C: EEYLQAFTY, self peptide from the ATP binding cassette protein ABCD3
D: LC13 TCR alpha chain
E: LC13 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)94,4105
Polymers94,4105
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-45 kcal/mol
Surface area38290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.518, 54.237, 121.766
Angle α, β, γ (deg.)90.000, 114.430, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDE

#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.: 1
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 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: 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.: 1
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.: 1
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, 28 molecules C

#3: Protein/peptide EEYLQAFTY, self peptide from the ATP binding cassette protein ABCD3


Mass: 1163.232 Da / Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
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: 2.7→50 Å / Num. obs: 21530 / % possible obs: 92 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.071 / Χ2: 1.68 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.820.29512780.98955.6
2.8-2.912.40.27618291.05578.7
2.91-3.042.90.23221461.16992.7
3.04-3.23.30.18322681.36598
3.2-3.43.50.14723351.74699.6
3.4-3.663.40.11522772.16298.6
3.66-4.033.40.08223032.02697.9
4.03-4.623.50.05623132.04998.6
4.62-5.813.60.04723501.90299.2
5.81-503.60.0324311.332100

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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: 2.7→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 37.367 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1112 5.2 %RANDOM
Rwork0.193 ---
obs0.197 21528 91.36 %-
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: 71.95 Å2 / Biso mean: 36.988 Å2 / Biso min: 9.96 Å2
Baniso -1Baniso -2Baniso -3
1--2 Å20 Å2-3.01 Å2
2---1.29 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6657 0 0 27 6684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216838
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9399305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48923.876356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.266151096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0991552
X-RAY DIFFRACTIONr_chiral_restr0.0810.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025382
X-RAY DIFFRACTIONr_nbd_refined0.2080.22753
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24531
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.24
X-RAY DIFFRACTIONr_mcbond_it1.19334233
X-RAY DIFFRACTIONr_mcangle_it2.0656694
X-RAY DIFFRACTIONr_scbond_it3.35272989
X-RAY DIFFRACTIONr_scangle_it5.053102611
LS refinement shellResolution: 2.702→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 40 -
Rwork0.241 754 -
all-794 -
obs--46.73 %

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