+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10732 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of full-length CD20 in complex with Ofatumumab Fab | |||||||||
Map data | Structure of Human CD20 in complex with Ofatumumab | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation ...store-operated calcium entry / positive regulation of calcium ion import across plasma membrane / calcium ion import into cytosol / epidermal growth factor receptor binding / B cell activation / B cell proliferation / plasma membrane raft / immunoglobulin binding / humoral immune response / B cell differentiation / protein tetramerization / B cell receptor signaling pathway / response to bacterium / MHC class II protein complex binding / cell surface receptor signaling pathway / external side of plasma membrane / cell surface / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.73 Å | |||||||||
Authors | Kumar A / Fronzes R / Reyes N | |||||||||
Funding support | France, 1 items
| |||||||||
Citation | Journal: Science / Year: 2020 Title: Binding mechanisms of therapeutic antibodies to human CD20. Authors: Anand Kumar / Cyril Planchais / Rémi Fronzes / Hugo Mouquet / Nicolas Reyes / Abstract: Monoclonal antibodies (mAbs) targeting human antigen CD20 (cluster of differentiation 20) constitute important immunotherapies for the treatment of B cell malignancies and autoimmune diseases. Type I ...Monoclonal antibodies (mAbs) targeting human antigen CD20 (cluster of differentiation 20) constitute important immunotherapies for the treatment of B cell malignancies and autoimmune diseases. Type I and II therapeutic mAbs differ in B cell binding properties and cytotoxic effects, reflecting differential interaction mechanisms with CD20. Here we present 3.7- to 4.7-angstrom cryo-electron microscopy structures of full-length CD20 in complexes with prototypical type I rituximab and ofatumumab and type II obinutuzumab. The structures and binding thermodynamics demonstrate that upon binding to CD20, type II mAbs form terminal complexes that preclude recruitment of additional mAbs and complement components, whereas type I complexes act as molecular seeds to increase mAb local concentration for efficient complement activation. Among type I mAbs, ofatumumab complexes display optimal geometry for complement recruitment. The uncovered mechanisms should aid rational design of next-generation immunotherapies targeting CD20. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10732.map.gz | 38.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-10732-v30.xml emd-10732.xml | 19.4 KB 19.4 KB | Display Display | EMDB header |
Images | emd_10732.png | 71.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10732 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10732 | HTTPS FTP |
-Validation report
Summary document | emd_10732_validation.pdf.gz | 260.9 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_10732_full_validation.pdf.gz | 260 KB | Display | |
Data in XML | emd_10732_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10732 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10732 | HTTPS FTP |
-Related structure data
Related structure data | 6y92MC 6y90C 6y97C 6y9aC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_10732.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Structure of Human CD20 in complex with Ofatumumab | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Full-length human antigen CD20 in complex with Ofatumumab Fab
Entire | Name: Full-length human antigen CD20 in complex with Ofatumumab Fab |
---|---|
Components |
|
-Supramolecule #1: Full-length human antigen CD20 in complex with Ofatumumab Fab
Supramolecule | Name: Full-length human antigen CD20 in complex with Ofatumumab Fab type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|
-Supramolecule #2: Full-length human CD20
Supramolecule | Name: Full-length human CD20 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK-293F / Recombinant plasmid: pcDNA3.1+ |
-Supramolecule #3: Ofatumumab Fab
Supramolecule | Name: Ofatumumab Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Location in cell: extra cellular |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK-293F / Recombinant plasmid: IgG1 expression vector |
-Macromolecule #1: B-lymphocyte antigen CD20
Macromolecule | Name: B-lymphocyte antigen CD20 / type: protein_or_peptide / ID: 1 / Details: Full-length wild type human CD20 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Cell: B-lymphocyte |
Molecular weight | Theoretical: 19.914656 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: TQSFFMRESK TLGAVQIMNG LFHIALGGLL MIPAGIYAPI CVTVWYPLWG GIMYIISGSL LAATEKNSRK CLVKGKMIMN SLSLFAAIS GMILSIMDIL NIKISHFLKM ESLNFIRAHT PYINIYNCEP ANPSEKNSPS TQYCYSIQSL FLGILSVMLI F AFFQELVI AGIVENEWKR |
-Macromolecule #2: Ofatumumab Fab light chain
Macromolecule | Name: Ofatumumab Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.174719 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSNWPITFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: EIVLTQSPAT LSLSPGERAT LSCRASQSVS SYLAWYQQKP GQAPRLLIYD ASNRATGIPA RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QRSNWPITFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNR |
-Macromolecule #3: Ofatumumab Fab heavy chain
Macromolecule | Name: Ofatumumab Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.138934 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVQPGRSLRL SCAASGFTFN DYAMHWVRQA PGKGLEWVST ISWNSGSIGY ADSVKGRFTI SRDNAKKSLY LQMNSLRAE DTALYYCAKD IQYGNYYYGM DVWGQGTTVT VSSASTKGPS VFPLAPGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String: EVQLVESGGG LVQPGRSLRL SCAASGFTFN DYAMHWVRQA PGKGLEWVST ISWNSGSIGY ADSVKGRFTI SRDNAKKSLY LQMNSLRAE DTALYYCAKD IQYGNYYYGM DVWGQGTTVT VSSASTKGPS VFPLAPGGTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKKVEP |
-Macromolecule #4: CHOLESTEROL HEMISUCCINATE
Macromolecule | Name: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: Y01 |
---|---|
Molecular weight | Theoretical: 486.726 Da |
Chemical component information | ChemComp-Y01: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.2 mg/mL | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.4 Component:
| |||||||||||||||
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2540 / Average exposure time: 40.0 sec. / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 0.8 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Cooling holder cryogen: NITROGEN |