+Open data
-Basic information
Entry | Database: PDB / ID: 6rv6 | |||||||||
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Title | Structure of properdin lacking TSR3 based on anomalous data | |||||||||
Components | (Properdin) x 2 | |||||||||
Keywords | IMMUNE SYSTEM / innate immunity / complement / protease / regulator | |||||||||
Function / homology | Function and homology information cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / specific granule lumen ...cytoplasmic side of Golgi membrane / positive regulation of opsonization / Defective B3GALTL causes PpS / O-glycosylation of TSR domain-containing proteins / Alternative complement activation / Activation of C3 and C5 / complement activation, alternative pathway / complement activation / Regulation of Complement cascade / specific granule lumen / positive regulation of immune response / tertiary granule lumen / defense response to bacterium / immune response / endoplasmic reticulum lumen / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.507 Å | |||||||||
Authors | Pedersen, D.V. / Andersen, G.R. | |||||||||
Funding support | Denmark, 1items
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Citation | Journal: Front Immunol / Year: 2019 Title: Structural Basis for Properdin Oligomerization and Convertase Stimulation in the Human Complement System. Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / ...Authors: Pedersen, D.V. / Gadeberg, T.A.F. / Thomas, C. / Wang, Y. / Joram, N. / Jensen, R.K. / Mazarakis, S.M.M. / Revel, M. / El Sissy, C. / Petersen, S.V. / Lindorff-Larsen, K. / Thiel, S. / Laursen, N.S. / Fremeaux-Bacchi, V. / Andersen, G.R. #1: Journal: Febs Lett. / Year: 2019 Title: Crystal structure of peptide-bound neprilysin reveals key binding interactions. Authors: Moss, S. / Subramanian, V. / Acharya, K.R. #2: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2019 Title: Crystallization and X-ray analysis of monodisperse human properdin. Authors: Pedersen, D.V. / Revel, M. / Gadeberg, T.A.F. / Andersen, G.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rv6.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rv6.ent.gz | 145.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rv6_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6rv6_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6rv6_validation.xml.gz | 17.1 KB | Display | |
Data in CIF | 6rv6_validation.cif.gz | 22.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/6rv6 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/6rv6 | HTTPS FTP |
-Related structure data
Related structure data | 6ru3C 6ru5C 6rurC 6rusC 6ruvC 6sejC C: citing same article (ref.) |
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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
#1: Protein | Mass: 18636.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TB-TSR1-TSR2 and additional residues from expression vector Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEL293F / References: UniProt: P27918 | ||||
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#2: Protein | Mass: 24724.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: TSR4-5-6 with addiotional residues from expression vector Source: (gene. exp.) Homo sapiens (human) / Gene: CFP, PFC / Production host: Homo sapiens (human) / Variant (production host): HEK293F / References: UniProt: P27918 | ||||
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...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 #5: Sugar | ChemComp-MAN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 6.61 Å3/Da / Density % sol: 81.38 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 1.0 M lithium sulfate, 0.1 M sodium acetate pH 4.0, 0.1 M barium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 2.47968 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.47968 Å / Relative weight: 1 |
Reflection | Resolution: 3.507→155 Å / Num. obs: 27811 / % possible obs: 99.9 % / Redundancy: 20.07 % / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 3.507→3.6 Å / Num. unique obs: 2051 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: electron density for TB-TSR1-TSR5-TSR6 Resolution: 3.507→77.707 Å / SU ML: 0.6 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.39
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.507→77.707 Å
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Refine LS restraints |
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LS refinement shell |
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