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- PDB-6rsy: The complex between TCR a7b2 and human Class I MHC HLA-A0201-WT1 ... -

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Basic information

Entry
Database: PDB / ID: 6rsy
TitleThe complex between TCR a7b2 and human Class I MHC HLA-A0201-WT1 with the bound RMFPNAPYL peptide.
Components
  • ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
  • Beta-2-microglobulinBeta-2 microglobulin
  • DMF4 Beta CHAIN
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • a7b2 ALPHA CHAIN
KeywordsIMMUNE SYSTEM / MHC CLASS I ANTIGEN- TCR - peptide complex
Function / homology
Function and homology information


posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / : / negative regulation of female gonad development / positive regulation of heart growth ...posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / : / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development / glomerular basement membrane development / diaphragm development / sex determination / mesenchymal to epithelial transition / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / positive regulation of male gonad development / cellular response to gonadotropin stimulus / Transcriptional regulation of testis differentiation / gonad development / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / hemi-methylated DNA-binding / tissue development / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / branching involved in ureteric bud morphogenesis / adrenal gland development / germ cell development / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / 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 / CD8 receptor binding / vasculogenesis / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / cellular response to cAMP / 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 / epithelial cell differentiation / detection of bacterium / T cell receptor binding / RNA splicing / 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 / kidney development / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / 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 / negative regulation of cell growth / 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 / positive regulation of miRNA transcription / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / male gonad development / 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 / positive regulation of immune response
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...Wilm's tumour protein, N-terminal / Wilm's tumour protein / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / 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 / Zinc finger C2H2-type / 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 class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Wilms tumor protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsSrikannathasan, V. / Robinson, R.A.
CitationJournal: J.Clin.Invest. / Year: 2020
Title: Specificity of bispecific T cell receptors and antibodies targeting peptide-HLA.
Authors: Holland, C.J. / Crean, R.M. / Pentier, J.M. / de Wet, B. / Lloyd, A. / Srikannathasan, V. / Lissin, N. / Lloyd, K.A. / Blicher, T.H. / Conroy, P.J. / Hock, M. / Pengelly, R.J. / Spinner, T.E. ...Authors: Holland, C.J. / Crean, R.M. / Pentier, J.M. / de Wet, B. / Lloyd, A. / Srikannathasan, V. / Lissin, N. / Lloyd, K.A. / Blicher, T.H. / Conroy, P.J. / Hock, M. / Pengelly, R.J. / Spinner, T.E. / Cameron, B. / Potter, E.A. / Jeyanthan, A. / Molloy, P.E. / Sami, M. / Aleksic, M. / Liddy, N. / Robinson, R.A. / Harper, S. / Lepore, M. / Pudney, C.R. / van der Kamp, M.W. / Rizkallah, P.J. / Jakobsen, B.K. / Vuidepot, A. / Cole, D.K.
History
DepositionMay 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 13, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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: ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
D: a7b2 ALPHA CHAIN
E: DMF4 Beta CHAIN
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
I: a7b2 ALPHA CHAIN
J: DMF4 Beta CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,37813
Polymers192,19210
Non-polymers1863
Water2,810156
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
D: a7b2 ALPHA CHAIN
E: DMF4 Beta CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2207
Polymers96,0965
Non-polymers1242
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-42 kcal/mol
Surface area37400 Å2
MethodPISA
2
F: HLA class I histocompatibility antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU
I: a7b2 ALPHA CHAIN
J: DMF4 Beta CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,1586
Polymers96,0965
Non-polymers621
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint-48 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.610, 114.750, 185.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21F
12B
22G
13D
23I
14E
24J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A2 - 274
2010F2 - 274
1020B1 - 100
2020G1 - 100
1030D3 - 191
2030I3 - 191
1040E4 - 245
2040J4 - 245

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

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


Mass: 31951.316 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Homo sapiens / 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 / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BETA-2-MICROGLOBULIN / Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein a7b2 ALPHA CHAIN


Mass: 23081.580 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: few N-terminal residues missing in the structure and also C-terminal residues.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein DMF4 Beta CHAIN


Mass: 28074.318 Da / Num. of mol.: 2
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 , 1 types, 2 molecules CH

#3: Protein/peptide ARG-MET-PHE-PRO-ASN-ALA-PRO-TYR-LEU


Mass: 1109.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Peptide, synthesized / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19544*PLUS

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Non-polymers , 2 types, 159 molecules

#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 7.5% PEG 8 K , 0.75 M NaCl , 50mM HEPES , pH 7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 2.95→114.75 Å / Num. obs: 43245 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.346 / Net I/σ(I): 8.8
Reflection shellResolution: 2.95→3 Å / Redundancy: 14 % / Rmerge(I) obs: 2.016 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 43245 / CC1/2: 0.524 / % possible all: 99.95

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
xia2data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→97.76 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.884 / SU B: 27.985 / SU ML: 0.485 / Cross valid method: THROUGHOUT / ESU R Free: 0.497 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29115 2242 5.2 %RANDOM
Rwork0.25066 ---
obs0.25275 40937 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.426 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å2-0 Å20 Å2
2--7.12 Å2-0 Å2
3----3.57 Å2
Refinement stepCycle: 1 / Resolution: 2.95→97.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13040 0 12 156 13208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01313414
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711633
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.65318234
X-RAY DIFFRACTIONr_angle_other_deg1.3441.57726988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79651626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34921.811784
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.019152114
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.13515102
X-RAY DIFFRACTIONr_chiral_restr0.0580.21707
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023034
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_it3.2038.0116531
X-RAY DIFFRACTIONr_mcbond_other3.2028.016530
X-RAY DIFFRACTIONr_mcangle_it5.41112.0068148
X-RAY DIFFRACTIONr_mcangle_other5.4112.0088149
X-RAY DIFFRACTIONr_scbond_it2.7498.136883
X-RAY DIFFRACTIONr_scbond_other2.7498.136884
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.74612.12210087
X-RAY DIFFRACTIONr_long_range_B_refined10.38651540
X-RAY DIFFRACTIONr_long_range_B_other10.38351528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A80780.15
12F80780.15
21B28490.14
22G28490.14
31D48580.18
32I48580.18
41E72250.14
42J72250.14
LS refinement shellResolution: 2.95→3.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 141 -
Rwork0.354 2978 -
obs--99.87 %

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