[English] 日本語
Yorodumi- EMDB-29077: Cryo-EM structure of the STAR-0215 Fab in complex with active hum... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29077 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the STAR-0215 Fab in complex with active human plasma kallikrein | |||||||||
Map data | Relion Refine3D full map | |||||||||
Sample |
| |||||||||
Keywords | plasma kallikrein / Plasma prekallikrein / Fletcher factor / hereditary angioedema / HAE / Kininogenin / C1-INH / Bradykinin / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Activation of Matrix Metalloproteinases / Defective factor XII causes hereditary angioedema / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation ...plasma kallikrein / Factor XII activation / Defective SERPING1 causes hereditary angioedema / positive regulation of fibrinolysis / zymogen activation / plasminogen activation / Activation of Matrix Metalloproteinases / Defective factor XII causes hereditary angioedema / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.62 Å | |||||||||
Authors | Fuller JR / Biris N / Bista P | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: J Pharmacol Exp Ther / Year: 2023 Title: STAR-0215 is a Novel, Long-Acting Monoclonal Antibody Inhibitor of Plasma Kallikrein for the Potential Treatment of Hereditary Angioedema. Authors: Vahe Bedian / Nikolaos Biris / Charles Omer / Jou-Ku Chung / James Fuller / Rafif Dagher / Sachin Chandran / Peter Harwin / Tomas Kiselak / Jonathan Violin / Andrew Nichols / Pradeep Bista / Abstract: Hereditary angioedema (HAE) is a rare autosomal dominant disorder caused by a deficiency in functional C1 esterase inhibitor, a serpin family protein that blocks the activity of plasma kallikrein. ...Hereditary angioedema (HAE) is a rare autosomal dominant disorder caused by a deficiency in functional C1 esterase inhibitor, a serpin family protein that blocks the activity of plasma kallikrein. Insufficient inhibition of plasma kallikrein results in the overproduction of bradykinin, a vasoactive inflammatory mediator that produces both pain and unpredictable swelling during HAE attacks, with potentially life-threatening consequences. We describe the generation of STAR-0215, a humanized IgG1 antibody with a long circulating half-life (t) that potently inhibits plasma kallikrein activity, with a >1000-fold lower affinity for prekallikrein and no measurable inhibitory activity against other serine proteases. The high specificity and inhibitory effect of STAR-0215 is demonstrated through a unique allosteric mechanism involving N-terminal catalytic domain binding, destabilization of the activation domain, and reversion of the active site to the inactive zymogen state. The YTE (M252Y/S254T/T256E) modified fragment crystallizable (Fc) domain of STAR-0215 enhances pH-dependent neonatal Fc receptor binding, resulting in a prolonged t in vivo (∼34 days in cynomolgus monkeys) compared with antibodies without this modification. A single subcutaneous dose of STAR-0215 (≥100 mg) was predicted to be active in patients for 3 months or longer, based on simulations using a minimal physiologically based pharmacokinetic model. These data indicate that STAR-0215, a highly potent and specific antibody against plasma kallikrein with extended t, is a potential agent for long-term preventative HAE therapy administered every 3 months or less frequently. SIGNIFICANCE STATEMENT: STAR-0215 is a YTE-modified immunoglobulin G1 monoclonal antibody with a novel binding mechanism that specifically and potently inhibits the enzymatic activity of plasma kallikrein and prevents the generation of bradykinin. It has been designed to be a long-lasting prophylactic treatment to prevent attacks of HAE and to decrease the burden of disease and the burden of treatment for people with HAE. | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_29077.map.gz | 131.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-29077-v30.xml emd-29077.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29077_fsc.xml | 12.4 KB | Display | FSC data file |
Images | emd_29077.png | 111 KB | ||
Masks | emd_29077_msk_1.map | 166.4 MB | Mask map | |
Filedesc metadata | emd-29077.cif.gz | 7.4 KB | ||
Others | emd_29077_additional_1.map.gz emd_29077_half_map_1.map.gz emd_29077_half_map_2.map.gz | 101.6 MB 131.2 MB 131.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29077 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29077 | HTTPS FTP |
-Validation report
Summary document | emd_29077_validation.pdf.gz | 690.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_29077_full_validation.pdf.gz | 690.2 KB | Display | |
Data in XML | emd_29077_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | emd_29077_validation.cif.gz | 26.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29077 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29077 | HTTPS FTP |
-Related structure data
Related structure data | 8fgxMC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_29077.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion Refine3D full map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.827 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | emd_29077_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Relion sharpened (B-factor -49.9834) and local resolution filtered...
File | emd_29077_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion sharpened (B-factor -49.9834) and local resolution filtered map. The model was refined primarily against this map, including ADPs. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Relion Refine3D half-map 1
File | emd_29077_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion Refine3D half-map 1 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Relion Refine3D half-map 2
File | emd_29077_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Relion Refine3D half-map 2 | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of STAR-0215 Fab with active plasma kallikrein
Entire | Name: Complex of STAR-0215 Fab with active plasma kallikrein |
---|---|
Components |
|
-Supramolecule #1: Complex of STAR-0215 Fab with active plasma kallikrein
Supramolecule | Name: Complex of STAR-0215 Fab with active plasma kallikrein type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: STAR-0215 Light chain
Macromolecule | Name: STAR-0215 Light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.540182 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCKASQDVG IAVAWYQQKP GKAPKFLIYY ASHRGWGVPD RFSGSGSGTD FTLTISSLQP EDFATYFCQ QYRSYPLTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASVGDRVT ITCKASQDVG IAVAWYQQKP GKAPKFLIYY ASHRGWGVPD RFSGSGSGTD FTLTISSLQP EDFATYFCQ QYRSYPLTFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #2: STAR-0215 Heavy chain
Macromolecule | Name: STAR-0215 Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.750527 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: QVQLVQSGAE VKKPGSSVKV SCKASGYAFS SYWMNWVRQA PGQGLEWIGQ IYPGDDDTNY NAKFQGRVTI TVDKSTTTAY MELSSLRSE DTAVYFCAGS LMVTTGAPFD YWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: QVQLVQSGAE VKKPGSSVKV SCKASGYAFS SYWMNWVRQA PGQGLEWIGQ IYPGDDDTNY NAKFQGRVTI TVDKSTTTAY MELSSLRSE DTAVYFCAGS LMVTTGAPFD YWGQGTTVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKR VEPKSC |
-Macromolecule #3: Plasma kallikrein light chain
Macromolecule | Name: Plasma kallikrein light chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
---|---|
Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 69.285984 KDa |
Sequence | String: GCLTQLYENA FFRGGDVASM YTPNAQYCQM RCTFHPRCLL FSFLPASSIN DMEKRFGCFL KDSVTGTLPK VHRTGAVSGH SLKQCGHQI SACHRDIYKG VDMRGVNFNV SKVSSVEECQ KRCTNNIRCQ FFSYATQTFH KAEYRNNCLL KYSPGGTPTA I KVLSNVES ...String: GCLTQLYENA FFRGGDVASM YTPNAQYCQM RCTFHPRCLL FSFLPASSIN DMEKRFGCFL KDSVTGTLPK VHRTGAVSGH SLKQCGHQI SACHRDIYKG VDMRGVNFNV SKVSSVEECQ KRCTNNIRCQ FFSYATQTFH KAEYRNNCLL KYSPGGTPTA I KVLSNVES GFSLKPCALS EIGCHMNIFQ HLAFSDVDVA RVLTPDAFVC RTICTYHPNC LFFTFYTNVW KIESQRNVCL LK TSESGTP SSSTPQENTI SGYSLLTCKR TLPEPCHSKI YPGVDFGGEE LNVTFVKGVN VCQETCTKMI RCQFFTYSLL PED CKEEKC KCFLRLSMDG SPTRIAYGTQ GSSGYSLRLC NTGDNSVCTT KTSTRIVGGT NSSWGEWPWQ VSLQVKLTAQ RHLC GGSLI GHQWVLTAAH CFDGLPLQDV WRIYSGILNL SDITKDTPFS QIKEIIIHQN YKVSEGNHDI ALIKLQAPLN YTEFQ KPIC LPSKGDTSTI YTNCWVTGWG FSKEKGEIQN ILQKVNIPLV TNEECQKRYQ DYKITQRMVC AGYKEGGKDA CKGDSG GPL VCKHNGMWRL VGITSWGEGC ARREQPGVYT KVAEYMDWIL EKTQSSDGKA QMQSPA UniProtKB: Plasma kallikrein |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG |
---|---|
Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.7 mg/mL |
---|---|
Buffer | pH: 7 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV Details: Grids were prepared using a ThermoFisher Vitrobot MkIV with the chamber held at 18C and 100% relative humidity. 3.5 uL of the sample was applied to an UltrAuFoil 1.2/1.3 300 mesh grid that ...Details: Grids were prepared using a ThermoFisher Vitrobot MkIV with the chamber held at 18C and 100% relative humidity. 3.5 uL of the sample was applied to an UltrAuFoil 1.2/1.3 300 mesh grid that had been freshly glow discharged, blotted for 4 seconds, and plunge frozen in liquid ethane.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3094 / Average exposure time: 4.88 sec. / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |
---|---|
Output model | PDB-8fgx: |