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Yorodumi- PDB-1orq: X-ray structure of a voltage-dependent potassium channel in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1orq | ||||||
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Title | X-ray structure of a voltage-dependent potassium channel in complex with an Fab | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / potassium channel / voltage-dependent / KvAP / Fab complex | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / delayed rectifier potassium channel activity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / delayed rectifier potassium channel activity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport / phagocytosis, engulfment / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / voltage-gated potassium channel complex / multivesicular body / B cell differentiation / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Aeropyrum pernix (archaea) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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 | 1orq.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1orq.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 1orq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1orq_validation.pdf.gz | 450.8 KB | Display | wwPDB validaton report |
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Full document | 1orq_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 1orq_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 1orq_validation.cif.gz | 38.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/or/1orq ftp://data.pdbj.org/pub/pdb/validation_reports/or/1orq | HTTPS FTP |
-Related structure data
Related structure data | 1orsC 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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Unit cell |
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Components on special symmetry positions |
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Details | The channel functions as tetramer. The remainder of the biological assembly is generated by the four fold axis: -x -y z, -y x z, y -x z. |
-Components
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 24271.910 Da / Num. of mol.: 1 / Fragment: KvAP / Mutation: Y46C 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 |
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-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 23527.826 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: 23781.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: mouse hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01865 |
-Non-polymers , 3 types, 19 molecules
#4: Chemical | ChemComp-CD / #5: Chemical | ChemComp-K / #6: 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: 4.77 Å3/Da / Density % sol: 73.99 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG400, Cadmium chloride, Sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-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: Oct 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.937 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→30 Å / Num. all: 22626 / Num. obs: 22476 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.08 / Net I/σ(I): 18 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2 / Num. unique all: 22501 / Rsym value: 0.424 / % possible all: 95.2 |
Reflection | *PLUS Lowest resolution: 30 Å / Rmerge(I) obs: 0.08 |
Reflection shell | *PLUS % possible obs: 95.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb code 1BAF Resolution: 3.2→29.95 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 26.7975 Å2 / ksol: 0.252452 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.4 Å2
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Refine analyze | Luzzati coordinate error free: 0.49 Å / Luzzati sigma a free: 0.89 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→29.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Version: 1 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5.1 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 73.4 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.383 / % reflection Rfree: 5 % / Rfactor Rwork: 0.339 |