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Yorodumi- EMDB-16279: Structure of CEACAM5 A3-B3 domain in Complex with Tusamitamab Fab -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16279 | |||||||||
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Title | Structure of CEACAM5 A3-B3 domain in Complex with Tusamitamab Fab | |||||||||
Map data | Cryo EM map for the complex | |||||||||
Sample |
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Keywords | CEACAM5 / Tusamitamab / Cancer / cell adhesion / cryo-EM / small molecular weight / Fab / A3-B3 / human membrane protein | |||||||||
Function / homology | Function and homology information GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane ...GPI anchor binding / homotypic cell-cell adhesion / Post-translational modification: synthesis of GPI-anchored proteins / negative regulation of myotube differentiation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / homophilic cell adhesion via plasma membrane adhesion molecules / negative regulation of anoikis / side of membrane / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / negative regulation of apoptotic process / apoptotic process / cell surface / protein homodimerization activity / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus sp. (mice) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.11 Å | |||||||||
Authors | Kumar A / Bertrand T / Rapisarda C / Rak A | |||||||||
Funding support | France, 1 items
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Citation | Journal: Res Sq / Year: 2023 Title: Structural insights into epitope-paratope interactions of monoclonal antibody targeting CEACAM5-expressing tumors Authors: Rak A / Kumar A / Duffi F / Gagnaire M / Rapisarda C / Bertrand T | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16279.map.gz | 58.3 MB | EMDB map data format | |
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Header (meta data) | emd-16279-v30.xml emd-16279.xml | 19 KB 19 KB | Display Display | EMDB header |
Images | emd_16279.png | 80.5 KB | ||
Filedesc metadata | emd-16279.cif.gz | 6.4 KB | ||
Others | emd_16279_half_map_1.map.gz emd_16279_half_map_2.map.gz | 59.5 MB 59.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16279 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16279 | HTTPS FTP |
-Validation report
Summary document | emd_16279_validation.pdf.gz | 834.3 KB | Display | EMDB validaton report |
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Full document | emd_16279_full_validation.pdf.gz | 833.9 KB | Display | |
Data in XML | emd_16279_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_16279_validation.cif.gz | 14.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16279 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16279 | HTTPS FTP |
-Related structure data
Related structure data | 8bw0MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16279.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo EM map for the complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map A
File | emd_16279_half_map_1.map | ||||||||||||
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Annotation | Half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map B
File | emd_16279_half_map_2.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hCEACAM5-A3B3-Tusamitamab Fab complex
Entire | Name: hCEACAM5-A3B3-Tusamitamab Fab complex |
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Components |
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-Supramolecule #1: hCEACAM5-A3B3-Tusamitamab Fab complex
Supramolecule | Name: hCEACAM5-A3B3-Tusamitamab Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Human CEACAM5 a3-B3 domain in the comlex with the Tusamitamab Fab |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 70 KDa |
-Macromolecule #1: Tusamitamab Fab heavy Chain
Macromolecule | Name: Tusamitamab Fab heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus sp. (mice) |
Molecular weight | Theoretical: 24.833652 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLQESGPG LVKPGGSLSL SCAASGFVFS SYDMSWVRQT PERGLEWVAY ISSGGGITYA PSTVKGRFTV SRDNAKNTLY LQMNSLTSE DTAVYYCAAH YFGSSGPFAY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS ...String: EVQLQESGPG LVKPGGSLSL SCAASGFVFS SYDMSWVRQT PERGLEWVAY ISSGGGITYA PSTVKGRFTV SRDNAKNTLY LQMNSLTSE DTAVYYCAAH YFGSSGPFAY WGQGTLVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV S WNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCDKTHT HHHHHH |
-Macromolecule #2: Tusamitamab Light Chain
Macromolecule | Name: Tusamitamab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus sp. (mice) |
Molecular weight | Theoretical: 23.497072 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPAS LSASVGDRVT ITCRASENIF SYLAWYQQKP GKSPKLLVYN TRTLAEGVPS RFSGSGSGTD FSLTISSLQP EDFATYYCQ HHYGTPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPAS LSASVGDRVT ITCRASENIF SYLAWYQQKP GKSPKLLVYN TRTLAEGVPS RFSGSGSGTD FSLTISSLQP EDFATYYCQ HHYGTPFTFG SGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #3: Carcinoembryonic antigen-related cell adhesion molecule 5
Macromolecule | Name: Carcinoembryonic antigen-related cell adhesion molecule 5 type: protein_or_peptide / ID: 3 / Details: A3-B3 domain / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 20.883041 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ELPKPSISSN NSKPVEDKDA VAFTCEPEAQ NTTYLWWVNG QSLPVSPRLQ LSNGNRTLTL FNVTRNDARA YVCGIQNSVS ANRSDPVTL DVLYGPDTPI ISPPDSSYLS GANLNLSCHS ASNPSPQYSW RINGIPQQHT QVLFIAKITP NNNGTYACFV S NLATGRNN ...String: ELPKPSISSN NSKPVEDKDA VAFTCEPEAQ NTTYLWWVNG QSLPVSPRLQ LSNGNRTLTL FNVTRNDARA YVCGIQNSVS ANRSDPVTL DVLYGPDTPI ISPPDSSYLS GANLNLSCHS ASNPSPQYSW RINGIPQQHT QVLFIAKITP NNNGTYACFV S NLATGRNN SIVKSITVSA SGTSPGLSAH HHHHH UniProtKB: Carcinoembryonic antigen-related cell adhesion molecule 5 |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.87 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 1.0 X / Component - Name: D-PBS / Details: Dulbeccos phosphate buffered saline |
Grid | Model: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5072 / Average exposure time: 4.72 sec. / Average electron dose: 62.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Illumination mode: OTHER / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 240000 |
Sample stage | Cooling holder cryogen: NITROGEN |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8bw0: |