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Yorodumi- PDB-8r8d: Cryo-EM structure of coagulation factor beta-XIIa in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r8d | ||||||
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Title | Cryo-EM structure of coagulation factor beta-XIIa in complex with the garadacimab Fab fragment (symmetric dimer) | ||||||
Components |
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Keywords | BLOOD CLOTTING / Complex / coagulation / trypsin-like serine protease / hereditary angioedema (HAE) | ||||||
Function / homology | Function and homology information coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / misfolded protein binding / positive regulation of fibrinolysis / zymogen activation ...coagulation factor XIIa / plasma kallikrein-kinin cascade / Factor XII activation / Defective SERPING1 causes hereditary angioedema / response to misfolded protein / positive regulation of plasminogen activation / blood coagulation, intrinsic pathway / misfolded protein binding / positive regulation of fibrinolysis / zymogen activation / Defective factor XII causes hereditary angioedema / protein autoprocessing / positive regulation of blood coagulation / rough endoplasmic reticulum / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / protein processing / blood coagulation / collagen-containing extracellular matrix / serine-type endopeptidase activity / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||
Authors | Drulyte, I. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structural basis for inhibition of beta-FXIIa by garadacimab Authors: Drulyte, I. / Ghai, R. / Ow, S.Y. / Kapp, E.A. / Quek, A.J. / Panousis, C. / Wilson, M.J. / Nash, A.D. / Pelzing, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r8d.cif.gz | 175.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r8d.ent.gz | 133.4 KB | Display | PDB format |
PDBx/mmJSON format | 8r8d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r8d_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8r8d_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8r8d_validation.xml.gz | 40.3 KB | Display | |
Data in CIF | 8r8d_validation.cif.gz | 59.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r8/8r8d ftp://data.pdbj.org/pub/pdb/validation_reports/r8/8r8d | HTTPS FTP |
-Related structure data
Related structure data | 18999MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 26537.750 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F12 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P00748 #2: Antibody | Mass: 25120.281 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) #3: Antibody | Mass: 22762.174 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ternary complex of coagulation factor beta-XIIa with garadacimab Fab fragment and anti-LC-lambda VHH Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.174 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) / Strain: Expi293 |
Buffer solution | pH: 5.5 / Details: 10 mM Na Acetate, 100 mM NaCl pH 5.5 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Immediately before blotting and plunge freezing, fluorinated octyl maltoside (FOM) was added to the sample to the final concentration of 0.005%-0.01% (w/v) |
Specimen support | Details: plasma current 20 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 1250 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 4000 / Details: 2000 with 0.005% FOM and 2000 with 0.01% FOM |
EM imaging optics | Energyfilter name: TFS Selectris Details: Electron source E-CFEG (cold-FEG), energy filter Selectris X Energyfilter slit width: 10 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 271636 Details: Particles were picked from each of the datasets independently using a blob picker using 50-170 A diameter. 124767 particles were picked from the 0.005% FOM dataset and 146869 particles from ...Details: Particles were picked from each of the datasets independently using a blob picker using 50-170 A diameter. 124767 particles were picked from the 0.005% FOM dataset and 146869 particles from the 0.01% FOM dataset. | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135296 / Symmetry type: POINT |