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- EMDB-34871: Cryo-EM structure of biparatopic antibody Bp109-92 in complex wit... -
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Basic information
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Title | Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 | |||||||||||||||||||||||||||||||||
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![]() | TNFR2 / biparatopic antibody / antagonist / IMMUNE SYSTEM | |||||||||||||||||||||||||||||||||
Function / homology | ![]() glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / varicosity ...glial cell-neuron signaling / regulation of cytokine production involved in immune response / tumor necrosis factor receptor superfamily complex / pulmonary valve development / RNA destabilization / aortic valve development / tumor necrosis factor receptor activity / negative regulation of extracellular matrix constituent secretion / positive regulation of apoptotic process involved in morphogenesis / varicosity / regulation of T cell cytokine production / negative regulation of neuroinflammatory response / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / tumor necrosis factor binding / positive regulation of myelination / regulation of neuroinflammatory response / positive regulation of membrane protein ectodomain proteolysis / regulation of myelination / positive regulation of oligodendrocyte differentiation / detection of maltose stimulus / regulation of T cell proliferation / maltose transport complex / carbohydrate transport / Interleukin-10 signaling / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / specific granule membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / extrinsic apoptotic signaling pathway / tumor necrosis factor-mediated signaling pathway / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / TNFR2 non-canonical NF-kB pathway / cellular response to growth factor stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / outer membrane-bounded periplasmic space / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / periplasmic space / inflammatory response / immune response / membrane raft / neuronal cell body / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / perinuclear region of cytoplasm / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||||||||||||||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.63 Å | |||||||||||||||||||||||||||||||||
![]() | Akiba H / Fujita J / Ise T / Nishiyama K / Miyata T / Kato T / Namba K / Ohno H / Kamada H / Nagata S / Tsumoto K | |||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Development of a 1:1-binding biparatopic anti-TNFR2 antagonist by reducing signaling activity through epitope selection. Authors: Hiroki Akiba / Junso Fujita / Tomoko Ise / Kentaro Nishiyama / Tomoko Miyata / Takayuki Kato / Keiichi Namba / Hiroaki Ohno / Haruhiko Kamada / Satoshi Nagata / Kouhei Tsumoto / ![]() Abstract: Conventional bivalent antibodies against cell surface receptors often initiate unwanted signal transduction by crosslinking two antigen molecules. Biparatopic antibodies (BpAbs) bind to two different ...Conventional bivalent antibodies against cell surface receptors often initiate unwanted signal transduction by crosslinking two antigen molecules. Biparatopic antibodies (BpAbs) bind to two different epitopes on the same antigen, thus altering crosslinking ability. In this study, we develop BpAbs against tumor necrosis factor receptor 2 (TNFR2), which is an attractive immune checkpoint target. Using different pairs of antibody variable regions specific to topographically distinct TNFR2 epitopes, we successfully regulate the size of BpAb-TNFR2 immunocomplexes to result in controlled agonistic activities. Our series of results indicate that the relative positions of the two epitopes recognized by the BpAb are critical for controlling its signaling activity. One particular antagonist, Bp109-92, binds TNFR2 in a 1:1 manner without unwanted signal transduction, and its structural basis is determined using cryo-electron microscopy. This antagonist suppresses the proliferation of regulatory T cells expressing TNFR2. Therefore, the BpAb format would be useful in designing specific and distinct antibody functions. | |||||||||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24 KB 24 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 8.4 KB | Display | ![]() |
Images | ![]() | 34.3 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7.3 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 870.3 KB | Display | ![]() |
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Full document | ![]() | 869.9 KB | Display | |
Data in XML | ![]() | 16.2 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hlbMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.0875 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of biparatopic antibody Bp109-92 in complex wit...
Entire | Name: Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 |
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Components |
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-Supramolecule #1: Cryo-EM structure of biparatopic antibody Bp109-92 in complex wit...
Supramolecule | Name: Cryo-EM structure of biparatopic antibody Bp109-92 in complex with TNFR2 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Tumor necrosis factor receptor superfamily member 1B,Maltose/malt...
Macromolecule | Name: Tumor necrosis factor receptor superfamily member 1B,Maltose/maltodextrin-binding periplasmic protein type: protein_or_peptide / ID: 1 Details: fusion protein of TNFR2 from human fused with MalE from E.Coli K-12 Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 60.447305 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: LPAQVAFTPY APEPGSTCRL REYYDQTAQM CCSKCSPGQH AKVFCTKTSD TVCDSCEDST YTQLWNWVPE CLSCGSRCSS DQVETQACT REQNRICTCR PGWYCALSKQ EGCRLCAPLR KCRPGFGVAR PGTETSDVVC KPCAPGTFSN TTSSTDICRP H QICNVVAI ...String: LPAQVAFTPY APEPGSTCRL REYYDQTAQM CCSKCSPGQH AKVFCTKTSD TVCDSCEDST YTQLWNWVPE CLSCGSRCSS DQVETQACT REQNRICTCR PGWYCALSKQ EGCRLCAPLR KCRPGFGVAR PGTETSDVVC KPCAPGTFSN TTSSTDICRP H QICNVVAI PGNASMDAVC KIEEGKLVIW INGDKGYNGL AEVGKKFEKD TGIKVTVEHP DKLEEKFPQV AATGDGPDII FW AHDRFGG YAQSGLLAEI TPDKAFQDKL YPFTWDAVRY NGKLIAYPIA VEALSLIYNK DLLPNPPKTW EEIPALDKEL KAK GKSALM FNLQEPYFTW PLIAADGGYA FKYENGKYDI KDVGVDNAGA KAGLTFLVDL IKNKHMNADT DYSIAEAAFN KGET AMTIN GPWAWSNIDT SKVNYGVTVL PTFKGQPSKP FVGVLSAGIN AASPNKELAK EFLENYLLTD EGLEAVNKDK PLGAV ALKS YEEELVKDPR IAATMENAQK GEIMPNIPQM SAFWYAVRTA VINAASGRQT VDEALKDAQG HHHHHH UniProtKB: Tumor necrosis factor receptor superfamily member 1B, Maltose/maltodextrin-binding periplasmic protein |
-Macromolecule #2: TR109 heavy chain
Macromolecule | Name: TR109 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.080273 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: QVQLKESGPG LVAPSQSLSI TCTVSGFSLT VYGVNWVRQP PGKGLEWLGM IWGDGSTAYN SALKSRLTIT KDNSKTQVFL KMNSLQTDD TARYYCARDG RRYALDYWGQ GTSVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH ...String: QVQLKESGPG LVAPSQSLSI TCTVSGFSLT VYGVNWVRQP PGKGLEWLGM IWGDGSTAYN SALKSRLTIT KDNSKTQVFL KMNSLQTDD TARYYCARDG RRYALDYWGQ GTSVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN S GALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKKVEPK SCFNTHTCPP CPAPELLG |
-Macromolecule #3: TR109 light chain
Macromolecule | Name: TR109 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.852311 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIVLTQSPTS LAVSLGQRAT ISCRASESVD SYGDSFLHWY QQKPGQPPIL LIYRASNLDS GIPARFSGSG SRTDFTLTIN PVEADDVAT YYCQQSNEDP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT ...String: DIVLTQSPTS LAVSLGQRAT ISCRASESVD SYGDSFLHWY QQKPGQPPIL LIYRASNLDS GIPARFSGSG SRTDFTLTIN PVEADDVAT YYCQQSNEDP YTFGGGTKLE IKRTVAAPSV FIFPPSDEQL KSGTASVVCL LNNFYPREAK VQWKVDNALQ S GNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC |
-Macromolecule #4: TR92 heavy chain
Macromolecule | Name: TR92 heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 25.543641 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: KVQLQQSGAE LVKPGASVKL SCKASGYTFT ESIIHWVKQR SGQGLEWIGW FYPGSDNINY NEKFKDKATL TADKSSSTVY MELTRLTSE DSAVYFCASH EGPYVYFDYW GQGTTLTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String: KVQLQQSGAE LVKPGASVKL SCKASGYTFT ESIIHWVKQR SGQGLEWIGW FYPGSDNINY NEKFKDKATL TADKSSSTVY MELTRLTSE DSAVYFCASH EGPYVYFDYW GQGTTLTVSS ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PKSCDKTHTC PPCPAPELLG |
-Macromolecule #5: TR92 light chain
Macromolecule | Name: TR92 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.590156 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: DIVMTQSHKF MSTSVGDRVS ITCKASQDVS TAVAWYQQKP GQSPKLLIYW TSTRHTGVPD RFTGSGSGTD YTLTISSVQA EDLALYYCQ HHYSTPYTFG GGTKLEIQRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIVMTQSHKF MSTSVGDRVS ITCKASQDVS TAVAWYQQKP GQSPKLLIYW TSTRHTGVPD RFTGSGSGTD YTLTISSVQA EDLALYYCQ HHYSTPYTFG GGTKLEIQRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.4 / Details: 1x PBS |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 4.9 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |