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Yorodumi- PDB-1ors: X-ray structure of the KvAP potassium channel voltage sensor in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ors | ||||||
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Title | X-ray structure of the KvAP potassium channel voltage sensor in complex with an Fab | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / potassium channel / voltage-dependent / voltage sensor / KvAP / Fab complex | ||||||
Function / homology | Function and homology information Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / delayed rectifier potassium channel activity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / delayed rectifier potassium channel activity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / voltage-gated potassium channel complex / B cell differentiation / complement activation, classical pathway / antigen binding / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / identical protein binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Jiang, Y. / Lee, A. / Chen, J. / Ruta, V. / Cadene, M. / Chait, B.T. / MacKinnon, R. | ||||||
Citation | Journal: Nature / Year: 2003 Title: X-ray structure of a voltage-dependent K+ channel Authors: Jiang, Y. / Lee, A. / Chen, J. / Ruta, V. / Cadene, M. / Chait, B.T. / MacKinnon, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ors.cif.gz | 130.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ors.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 1ors.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ors_validation.pdf.gz | 445.4 KB | Display | wwPDB validaton report |
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Full document | 1ors_full_validation.pdf.gz | 465.9 KB | Display | |
Data in XML | 1ors_validation.xml.gz | 28.3 KB | Display | |
Data in CIF | 1ors_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1ors ftp://data.pdbj.org/pub/pdb/validation_reports/or/1ors | HTTPS FTP |
-Related structure data
Related structure data | 1orqC 1bafS 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
#1: Antibody | Mass: 23409.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837 |
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#2: Antibody | Mass: 24043.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869 |
#3: Protein | Mass: 14629.464 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9YDF8 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG4000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.937 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30 Å / Num. all: 58711 / Num. obs: 56778 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.058 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 5415 / Rsym value: 0.177 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb code 1BAF Resolution: 1.9→30 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Displacement parameters | Biso mean: 34.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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