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- PDB-6rpa: Crystal structure of the T-cell receptor NYE_S2 bound to HLA A2*0... -

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Basic information

Entry
Database: PDB / ID: 6rpa
TitleCrystal structure of the T-cell receptor NYE_S2 bound to HLA A2*01-SLLMWITQV
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Heteroclitic NY-ESO-1 157-165 peptide
KeywordsIMMUNE SYSTEM / T-cell receptor / peptide-Human leukocyte antigen complex / NY-ESO-1 / cancer testis antigen
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna ...tRNA threonylcarbamoyladenosine metabolic process / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / CD8 receptor binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / detection of bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / T cell receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / 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 erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of type II interferon production / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / T cell receptor signaling pathway / negative regulation of neuron projection development / E3 ubiquitin ligases ubiquitinate target proteins / antibacterial humoral response / ER-Phagosome pathway / protein refolding / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / signaling receptor binding / external side of plasma membrane / innate immune response / lysosomal membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / :
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / 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 / : ...CTAG/Pcc1 family / Transcription factor Pcc1 / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Cancer/testis antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsColes, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. ...Coles, C.H. / Mulvaney, R. / Malla, S. / Lloyd, A. / Smith, K. / Chester, F. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Vuidepot, A. / Jakobsen, B.K. / Harper, S.
CitationJournal: J Immunol. / Year: 2020
Title: TCRs with Distinct Specificity Profiles Use Different Binding Modes to Engage an Identical Peptide-HLA Complex.
Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / ...Authors: Coles, C.H. / Mulvaney, R.M. / Malla, S. / Walker, A. / Smith, K.J. / Lloyd, A. / Lowe, K.L. / McCully, M.L. / Martinez Hague, R. / Aleksic, M. / Harper, J. / Paston, S.J. / Donnellan, Z. / Chester, F. / Wiederhold, K. / Robinson, R.A. / Knox, A. / Stacey, A.R. / Dukes, J. / Baston, E. / Griffin, S. / Jakobsen, B.K. / Vuidepot, A. / Harper, S.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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
Revision 1.4Nov 20, 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, A-2 alpha chain
B: Beta-2-microglobulin
C: Heteroclitic NY-ESO-1 157-165 peptide
D: T-cell receptor alpha chain
E: T-cell receptor beta chain


Theoretical massNumber of molelcules
Total (without water)95,8685
Polymers95,8685
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-49 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.160, 84.250, 111.510
Angle α, β, γ (deg.)90.00, 129.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 32082.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769

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T-cell receptor ... , 2 types, 2 molecules DE

#4: Protein T-cell receptor alpha chain


Mass: 23422.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein T-cell receptor beta chain


Mass: 27392.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 50 molecules C

#3: Protein/peptide Heteroclitic NY-ESO-1 157-165 peptide


Mass: 1090.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 3.26 Å3/Da / Density % sol: 62.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.02 M sodium/potassium phosphate, 20 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.56→66.51 Å / Num. obs: 37679 / % possible obs: 99.3 % / Redundancy: 7.66 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.025 / Net I/σ(I): 17.9
Reflection shellResolution: 2.56→2.6 Å / Redundancy: 7.94 % / Rmerge(I) obs: 2.07 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1945 / CC1/2: 0.637 / Rpim(I) all: 0.775 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia20.5.436-g557f8872-dials-1.7data reduction
xia20.5.436-g557f8872-dials-1.7data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e00 (chains A and B), 3REV (chain A) and 4DZB (chain B)

5e00

3rev

4dzb


Resolution: 2.56→66.51 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.147 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R: 0.466 / ESU R Free: 0.314 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29324 1945 4.9 %RANDOM
Rwork0.2499 ---
obs0.25209 37679 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 80.735 Å2
Baniso -1Baniso -2Baniso -3
1-3.15 Å20 Å2-3.46 Å2
2--3.12 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.56→66.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6277 0 0 49 6326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0196444
X-RAY DIFFRACTIONr_bond_other_d0.0010.025656
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9338752
X-RAY DIFFRACTIONr_angle_other_deg0.846313157
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0765776
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19724.006322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.575151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3611541
X-RAY DIFFRACTIONr_chiral_restr0.0720.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021370
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2568.2463131
X-RAY DIFFRACTIONr_mcbond_other3.2538.2453130
X-RAY DIFFRACTIONr_mcangle_it5.42712.353898
X-RAY DIFFRACTIONr_mcangle_other5.42712.3513899
X-RAY DIFFRACTIONr_scbond_it2.6068.3213313
X-RAY DIFFRACTIONr_scbond_other2.6058.3223314
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.54112.4244855
X-RAY DIFFRACTIONr_long_range_B_refined9.72723647
X-RAY DIFFRACTIONr_long_range_B_other9.72723645
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.56→2.626 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 142 -
Rwork0.429 2745 -
obs--98.97 %

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