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Yorodumi- PDB-8che: TLT-1 binding Fab of the bispecific antibody HMB-001 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8che | ||||||
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Title | TLT-1 binding Fab of the bispecific antibody HMB-001 in complex with the TLT-1 stalk peptide | ||||||
Components |
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Keywords | BLOOD CLOTTING / TLT-1 / Fab / Bispecific Antibody / HMB-001 | ||||||
Function / homology | Function and homology information platelet alpha granule / calcium-mediated signaling / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / nuclear speck / innate immune response / cell surface / Golgi apparatus / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Johansson, E. / Schluckebier, G. | ||||||
Funding support | 1items
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Citation | Journal: Nat Cardiovasc Res / Year: 2024 Title: A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders Authors: Gandhi, P.S. / Zivkovic, M. / Ostergaard, H. / Bonde, A.C. / Elm, T. / Lovgreen, M.N. / Schluckebier, G. / Johansson, E. / Olsen, O.H. / Olsen, E.H.N. / de Bus, I.A. / Bloem, K. / Alskar, O. ...Authors: Gandhi, P.S. / Zivkovic, M. / Ostergaard, H. / Bonde, A.C. / Elm, T. / Lovgreen, M.N. / Schluckebier, G. / Johansson, E. / Olsen, O.H. / Olsen, E.H.N. / de Bus, I.A. / Bloem, K. / Alskar, O. / Rea, C.J. / Bjorn, S.E. / Schutgens, R.E. / Sorensen, B. / Urbanus, R.T. / Faber, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8che.cif.gz | 626.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8che.ent.gz | 428.8 KB | Display | PDB format |
PDBx/mmJSON format | 8che.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8che_validation.pdf.gz | 462.6 KB | Display | wwPDB validaton report |
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Full document | 8che_full_validation.pdf.gz | 468.6 KB | Display | |
Data in XML | 8che_validation.xml.gz | 43.5 KB | Display | |
Data in CIF | 8che_validation.cif.gz | 66.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/8che ftp://data.pdbj.org/pub/pdb/validation_reports/ch/8che | HTTPS FTP |
-Related structure data
Related structure data | 8cn9C 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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2 |
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Unit cell |
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-Components
#1: Antibody | Mass: 22847.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 24213.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Protein/peptide | Mass: 3957.113 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YW5 #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1M lithium chloride, 20% (w/v) PEG 6000, 100 mM citric acid/NaOH, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→28.46 Å / Num. obs: 140068 / % possible obs: 91.03 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.72 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.05225 / Rpim(I) all: 0.05222 / Rrim(I) all: 0.07387 / Net I/σ(I): 9.03 |
Reflection shell | Resolution: 1.49→1.543 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5929 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 25651 / CC1/2: 0.0678 / CC star: 0.356 / Rpim(I) all: 0.5928 / Rrim(I) all: 0.8384 / % possible all: 62.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→28.46 Å / SU ML: 0.1661 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.0085 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→28.46 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -2.35225873292 Å / Origin y: -12.2897337815 Å / Origin z: -32.8803688976 Å
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Refinement TLS group | Selection details: all |