+Open data
-Basic information
Entry | Database: PDB / ID: 5b71 | ||||||
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Title | Crystal structure of complement C5 in complex with SKY59 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / pH-dependent / recycling antibody / complement C5 / Fab / Complex | ||||||
Function / homology | Function and homology information Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / Peptide ligand-binding receptors ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / Peptide ligand-binding receptors / complement activation, classical pathway / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.11 Å | ||||||
Authors | Irie, M. / Shimizu, Y. / Sampei, Z. / Fukuzawa, T. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Long lasting neutralization of C5 by SKY59, a novel recycling antibody, is a potential therapy for complement-mediated diseases. Authors: Fukuzawa, T. / Sampei, Z. / Haraya, K. / Ruike, Y. / Shida-Kawazoe, M. / Shimizu, Y. / Gan, S.W. / Irie, M. / Tsuboi, Y. / Tai, H. / Sakiyama, T. / Sakamoto, A. / Ishii, S. / Maeda, A. / ...Authors: Fukuzawa, T. / Sampei, Z. / Haraya, K. / Ruike, Y. / Shida-Kawazoe, M. / Shimizu, Y. / Gan, S.W. / Irie, M. / Tsuboi, Y. / Tai, H. / Sakiyama, T. / Sakamoto, A. / Ishii, S. / Maeda, A. / Iwayanagi, Y. / Shibahara, N. / Shibuya, M. / Nakamura, G. / Nambu, T. / Hayasaka, A. / Mimoto, F. / Okura, Y. / Hori, Y. / Habu, K. / Wada, M. / Miura, T. / Tachibana, T. / Honda, K. / Tsunoda, H. / Kitazawa, T. / Kawabe, Y. / Igawa, T. / Hattori, K. / Nezu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b71.cif.gz | 213.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b71.ent.gz | 168.7 KB | Display | PDB format |
PDBx/mmJSON format | 5b71.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b71 ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b71 | HTTPS FTP |
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-Related structure data
-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: 23328.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #2: Antibody | Mass: 24121.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human) #3: Protein | Mass: 12297.792 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 20-124 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: C5, CPAMD4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01031 #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: 2.29 Å3/Da / Density % sol: 46.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2M magnesium formate dehydrate, 15.0% w/v polyethylene glycol 3350, 20% v/v glycerol as cryoprotectant |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→42.49 Å / Num. obs: 56154 / % possible obs: 92.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.11→2.16 Å / Redundancy: 2 % / Rmerge(I) obs: 0.317 / Mean I/σ(I) obs: 1.8 / % possible all: 95.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BBJ, 3CU7 Resolution: 2.11→25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 9.455 / SU ML: 0.233 / SU R Cruickshank DPI: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.343 / ESU R Free: 0.247
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.33 Å2 / Biso mean: 38.604 Å2 / Biso min: 16.15 Å2
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Refinement step | Cycle: final / Resolution: 2.11→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.164 Å / Total num. of bins used: 20
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