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- PDB-7pbc: Crystal structure of engineered TCR (796) complexed to HLA-A*02:0... -

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Basic information

Entry
Database: PDB / ID: 7pbc
TitleCrystal structure of engineered TCR (796) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer peptide
Components
  • (T-cell receptor ...) x 2
  • Beta-2-microglobulinBeta-2 microglobulin
  • MHC class I antigen
  • Melanoma-associated antigen 10
KeywordsIMMUNE SYSTEM / T-cell receptor / human leukocyte antigen / immunoglobulin fold / complex
Function / homology
Function and homology information


antigen processing and presentation / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway ...antigen processing and presentation / 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 / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / histone deacetylase binding / 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 / sensory perception of smell / positive regulation of T cell activation / 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 / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / negative regulation of transcription by RNA polymerase II / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen ...Melanoma associated antigen, N-terminal / Melanoma associated antigen family N terminal / Melanoma associated antigen family N terminal / MAGE conserved domain profile. / MAGE homology domain / Melanoma-associated antigen / MAGE homology domain, winged helix WH1 motif / MAGE homology domain, winged helix WH2 motif / MAGE homology domain / Melanoma-associated antigen / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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
Similarity search - Domain/homology
Melanoma-associated antigen 10 / Beta-2-microglobulin / MHC class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsSimister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Adaptimmune Ltd United Kingdom
Citation
Journal: J Immunother Cancer / Year: 2022
Title: Structural insights into engineering a T-cell receptor targeting MAGE-A10 with higher affinity and specificity for cancer immunotherapy.
Authors: Simister, P.C. / Border, E.C. / Vieira, J.F. / Pumphrey, N.J.
#1: Journal: Oncoimmunology / Year: 2018
Title: Affinity-enhanced T-cell receptors for adoptive T-cell therapy targeting MAGE-A10: strategy for selection of an optimal candidate
Authors: Border, E.C. / Sanderson, J.P. / Weissensteiner, T. / Gerry, A.B. / Pumphrey, N.J.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
CCC: MHC class I antigen
DDD: Beta-2-microglobulin
AAA: T-cell receptor (TRAV/TRAC)
BBB: T-cell receptor (TRBV/TRBC)
EEE: Melanoma-associated antigen 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2989
Polymers94,9865
Non-polymers3124
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11200 Å2
ΔGint-60 kcal/mol
Surface area35770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.330, 77.500, 115.120
Angle α, β, γ (deg.)90.000, 102.880, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules CCCDDD

#1: Protein MHC class I antigen


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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q861F7
#2: Protein Beta-2-microglobulin / 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 AAABBB

#3: Protein T-cell receptor (TRAV/TRAC)


Mass: 22818.072 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)
#4: Protein T-cell receptor (TRBV/TRBC)


Mass: 27171.395 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 , 1 types, 1 molecules EEE

#5: Protein/peptide Melanoma-associated antigen 10 / / Cancer/testis antigen 1.10 / CT1.10 / MAGE-10 antigen


Mass: 1035.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P43363

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Non-polymers , 3 types, 350 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.4903 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium bromide, 0.1M Bis-Tris propane pH 8.5, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.04→77.5 Å / Num. obs: 59081 / % possible obs: 99.4 % / Redundancy: 2.9 % / CC1/2: 0.988 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.1 / Rrim(I) all: 0.145 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.12-77.52.90.0457090.9940.0430.062
2.04-2.092.80.73643510.7280.6811.005

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5.8.0267refinement
Aimless0.5.32data scaling
MOSFLMdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QEU, 1I4F

3qeu

1i4f


Resolution: 2.04→63.853 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.009 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.188 / ESU R Free: 0.171
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2361 2817 4.77 %Random
Rwork0.1865 56241 --
all0.189 ---
obs-59058 99.287 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.492 Å2
Baniso -1Baniso -2Baniso -3
1--2.622 Å2-0 Å2-0.639 Å2
2--0.64 Å2-0 Å2
3---2.059 Å2
Refinement stepCycle: LAST / Resolution: 2.04→63.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 19 346 6817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136659
X-RAY DIFFRACTIONr_bond_other_d0.0020.0175838
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6499069
X-RAY DIFFRACTIONr_angle_other_deg1.2641.57713418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5965821
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.11722.143364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26115989
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6981542
X-RAY DIFFRACTIONr_chiral_restr0.0630.2853
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027703
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021633
X-RAY DIFFRACTIONr_nbd_refined0.1950.21113
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.25412
X-RAY DIFFRACTIONr_nbtor_refined0.1650.23072
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3050.2353
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0290.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.216
X-RAY DIFFRACTIONr_nbd_other0.1540.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2580.211
X-RAY DIFFRACTIONr_mcbond_it2.5593.6493295
X-RAY DIFFRACTIONr_mcbond_other2.563.6493294
X-RAY DIFFRACTIONr_mcangle_it3.945.4594110
X-RAY DIFFRACTIONr_mcangle_other3.945.4594111
X-RAY DIFFRACTIONr_scbond_it3.0353.8563364
X-RAY DIFFRACTIONr_scbond_other3.0353.8563364
X-RAY DIFFRACTIONr_scangle_it4.6895.6964958
X-RAY DIFFRACTIONr_scangle_other4.6895.6964958
X-RAY DIFFRACTIONr_lrange_it6.60841.027143
X-RAY DIFFRACTIONr_lrange_other6.5940.9287091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.0930.312270.2894115X-RAY DIFFRACTION98.7042
2.093-2.150.2881790.2684084X-RAY DIFFRACTION99.6028
2.15-2.2130.2921770.2473903X-RAY DIFFRACTION99.1736
2.213-2.2810.2651780.2353860X-RAY DIFFRACTION99.6053
2.281-2.3550.2721920.2263695X-RAY DIFFRACTION99.3355
2.355-2.4380.2841670.213546X-RAY DIFFRACTION99.1985
2.438-2.530.2561730.2063436X-RAY DIFFRACTION99.3121
2.53-2.6330.2651810.1893304X-RAY DIFFRACTION99.1747
2.633-2.750.2471940.193167X-RAY DIFFRACTION99.4967
2.75-2.8840.2871400.183098X-RAY DIFFRACTION99.2338
2.884-3.040.2371630.1652864X-RAY DIFFRACTION99.051
3.04-3.2250.2311180.162774X-RAY DIFFRACTION99.211
3.225-3.4470.2021110.172592X-RAY DIFFRACTION99.6681
3.447-3.7230.2211300.1682409X-RAY DIFFRACTION99.3738
3.723-4.0780.2111050.162236X-RAY DIFFRACTION99.49
4.078-4.5580.1841360.1461988X-RAY DIFFRACTION99.206
4.558-5.2620.185740.1511792X-RAY DIFFRACTION99.5731
5.262-6.4410.276780.2071516X-RAY DIFFRACTION99.5006
6.441-9.0940.277510.1861195X-RAY DIFFRACTION99.2829
9.094-63.8530.18430.183667X-RAY DIFFRACTION99.7191

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