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- PDB-2bc9: Crystal-structure of the N-terminal large GTPase Domain of human ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bc9 | |||||||||
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Title | Crystal-structure of the N-terminal large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with non-hydrolysable GTP analogue GppNHp | |||||||||
![]() | Interferon-induced guanylate-binding protein 1 | |||||||||
![]() | SIGNALING PROTEIN / Protein- guanine nucleotide complex | |||||||||
Function / homology | ![]() GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production ...GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of protein localization to plasma membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / cytokine binding / defense response to protozoan / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / regulation of protein localization to plasma membrane / cellular response to interleukin-1 / regulation of calcium-mediated signaling / G protein activity / lipopolysaccharide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hsp90 protein binding / cytoplasmic vesicle membrane / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Ghosh, A. / Praefcke, G.J.K. / Renault, L. / Wittinghofer, A. / Herrmann, C. | |||||||||
![]() | ![]() Title: How guanylate-binding proteins achieve assembly-stimulated processive cleavage of GTP to GMP. Authors: Ghosh, A. / Praefcke, G.J. / Renault, L. / Wittinghofer, A. / Herrmann, C. #1: ![]() Title: Triphosphate structure of guanylate-binding protein 1 and implications for nucleotide binding and GTPase mechanism. Authors: Prakash, B. / Renault, L. / Praefcke, G.J. / Herrmann, C. / Wittinghofer, A. #2: ![]() Title: Structure of human guanylate-binding protein 1 representing a unique class of GTP-binding proteins. Authors: Prakash, B. / Praefcke, G.J. / Renault, L. / Herrmann, C. / Wittinghofer, A. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.9 KB | Display | ![]() |
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PDB format | ![]() | 53.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 773.5 KB | Display | ![]() |
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Full document | ![]() | 786.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2b8wSC ![]() 2b92C ![]() 2d4hC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Details | One of the subunit of homodimeric biological assembly is in the asymmetric unit |
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Components
#1: Protein | Mass: 37078.449 Da / Num. of mol.: 1 / Fragment: N-terminal Large GTPase doamin Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-GNP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.93 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 10 % Peg 3350, 100 mM NaSCN, 40 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 10, 2002 / Details: Ge (220) Crystal |
Radiation | Monochromator: Diamond monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 10831 / Num. obs: 10593 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.8→2.9 Å / % possible all: 98.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entry: 2B8W Resolution: 2.8→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å /
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