+Open data
-Basic information
Entry | Database: PDB / ID: 4bsv | |||||||||
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Title | Heterodimeric Fc Antibody Azymetric Variant 1 | |||||||||
Components | (HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT ...) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / ANTIBODY / BISPECIFIC / SCAFFOLD / ANTIBODY ENGINEERING / ZYMEWORKS INC. | |||||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Suits, M.D.L. / Spreter, T. / Cabrera, E.E. / Dixit, S.B. / Lario, P.I. / Poon, D.K.Y. / D'Angelo, I.E.P. / Boulanger, M.J. | |||||||||
Citation | Journal: Mabs / Year: 2013 Title: Improving Biophysical Properties of a Bispecific Antibody Scaffold to Aid Developability: Quality by Molecular Design. Authors: Von Kreudenstein, T.S. / Escobar-Carbrera, E. / Lario, P.I. / D'Angelo, I. / Brault, K. / Kelly, J. / Durocher, Y. / Baardsnes, J. / Woods, R.J. / Xie, M.H. / Girod, P. / Suits, M.D.L. / ...Authors: Von Kreudenstein, T.S. / Escobar-Carbrera, E. / Lario, P.I. / D'Angelo, I. / Brault, K. / Kelly, J. / Durocher, Y. / Baardsnes, J. / Woods, R.J. / Xie, M.H. / Girod, P. / Suits, M.D.L. / Boulanger, M.J. / Poon, D.K.Y. / Ng, G.Y.K. / Dixit, S.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bsv.cif.gz | 193.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bsv.ent.gz | 161.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bsv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/4bsv ftp://data.pdbj.org/pub/pdb/validation_reports/bs/4bsv | HTTPS FTP |
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-Related structure data
Related structure data | 4bswC 2j6eS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT ... , 2 types, 2 molecules AB
#1: Protein | Mass: 25301.643 Da / Num. of mol.: 1 / Fragment: IG GAMMA 1 FC DOMAIN, RESIDUES 106-330 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01857 |
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#2: Protein | Mass: 25490.941 Da / Num. of mol.: 1 / Fragment: IG GAMMA 1 FC DOMAIN, RESIDUES 106-330 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01857 |
-Sugars , 4 types, 4 molecules
#3: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose Source method: isolated from a genetically manipulated source |
#6: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 3 types, 765 molecules
#7: Chemical | ChemComp-EDO / #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | FC HETERODIMERS WERE CONSTRUCTED VIA INTRODUCTION OF THE FOLLOWING MUTATIONS - T350V, L351Y, F405A, ...FC HETERODIME |
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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: 2.55 Å3/Da / Density % sol: 51.82 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop Details: VIA HANGING DROP VAPOR DIFFUSION METHOD AT A RATIO OF 2:1 OF 8.5 MG/ML OF AZYMETRIC VARIANT ABOVE A MOTHER LIQUOR SOLUTION COMPOSED OF 5% (V/V) ETHYLENE GLYCOL, 18% (W/V) POLYETHYLENE GLYCOL ...Details: VIA HANGING DROP VAPOR DIFFUSION METHOD AT A RATIO OF 2:1 OF 8.5 MG/ML OF AZYMETRIC VARIANT ABOVE A MOTHER LIQUOR SOLUTION COMPOSED OF 5% (V/V) ETHYLENE GLYCOL, 18% (W/V) POLYETHYLENE GLYCOL 3350, AND 0.15 M AMMONIUM IODIDE WITH AID OF MICROSEEDING. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98005 |
Detector | Type: MARRESEARCH MX-300HE / Detector: CCD / Date: Sep 12, 2012 Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT) |
Radiation | Monochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98005 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→47 Å / Num. obs: 56316 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 26 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.9 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J6E Resolution: 1.75→41.38 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.746 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN ORDER TO ACCOMMODATE THE PERFECT 50-50 MIXTURE, RECIPROCAL RELATIONSHIP OF THE AZYMETRIC HETERODIMER PRESENT IN THE CRYSTALLOGRAPHIC ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN ORDER TO ACCOMMODATE THE PERFECT 50-50 MIXTURE, RECIPROCAL RELATIONSHIP OF THE AZYMETRIC HETERODIMER PRESENT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, TWO POSSIBLE HETERODIMER PAIRS, EACH WITH 0.5 ATOMIC OCCUPANCIES, WERE MODELED. FOR EXAMPLE, THE OCCUPANCY OF MOLECULE A CAN BE EQUALLY BE DESCRIBED BY MOLECULE B AND VICE VERSA.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.779 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→41.38 Å
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