|Entry||Database: PDB / ID: 2b92|
|Title||Crystal-structure of the N-terminal Large GTPase Domain of human Guanylate Binding protein 1 (hGBP1) in complex with GDP/AlF3|
|Components||Interferon-induced guanylate-binding protein 1|
|Keywords||SIGNALING PROTEIN / protein- guanine nucleotide complex|
|Function / homology|
Function and homology information
protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of interleukin-2 production / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / negative regulation of protein localization to plasma membrane / negative regulation of T cell receptor signaling pathway / cytokine binding / spectrin binding / regulation of calcium-mediated signaling / regulation of protein localization to plasma membrane ...protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / negative regulation of interleukin-2 production / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / negative regulation of protein localization to plasma membrane / negative regulation of T cell receptor signaling pathway / cytokine binding / spectrin binding / regulation of calcium-mediated signaling / regulation of protein localization to plasma membrane / vesicle membrane / cellular response to interleukin-1 / cellular response to interferon-gamma / negative regulation of ERK1 and ERK2 cascade / Hsp90 protein binding / GDP binding / Interferon gamma signaling / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / defense response to virus / cytoplasmic vesicle / GTPase activity / Golgi membrane / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Guanylate-binding protein, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, N-terminal domain / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / GB1/RHD3-type guanine nucleotide-binding (G) domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...Guanylate-binding protein, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, N-terminal domain / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / GB1/RHD3-type guanine nucleotide-binding (G) domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / Guanylate-binding protein 1
Similarity search - Component
|Biological species||Homo sapiens (human)|
|Method||X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å|
|Authors||Ghosh, A. / Praefcke, G.J.K. / Renault, L. / Wittinghofer, A. / Herrmann, C.|
Journal: Nature / Year: 2006
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: Journal: Embo J. / Year: 2000
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.
|Structure viewer||Molecule: |
Downloads & links
A: Interferon-induced guanylate-binding protein 1
B: Interferon-induced guanylate-binding protein 1
|Noncrystallographic symmetry (NCS)||NCS domain: |
NCS domain segments:
|Details||The biological assembly is the homodimer in the asymmetric unit|
Mass: 37078.449 Da / Num. of mol.: 2 / Fragment: N-terminal Large GTPase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Plasmid: pQE9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32455
|#2: Chemical||#3: Chemical|
Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
|#4: Chemical||#5: Water|| ChemComp-HOH / |
|Experiment||Method: X-RAY DIFFRACTION / Number of used crystals: 1|
|Crystal||Density Matthews: 3.14 Å3/Da / Density % sol: 60.78 %|
|Crystal grow||Temperature: 298 K|
Details: 12.5% Peg3350, 125mM Na2HPO4 (from Hampton Research peg/ion screen supplied at pH9.1), VAPOR DIFFUSION, HANGING DROP, temperature 298K
|Diffraction||Mean temperature: 100 K|
|Diffraction source||Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393|
|Detector||Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 15, 2002 / Details: GE(220) CRYSTAL|
|Radiation||Monochromator: DIAMOND MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray|
|Radiation wavelength||Wavelength: 0.9393 Å / Relative weight: 1|
|Reflection||Resolution: 3.2→30 Å / Num. obs: 14438 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 90.1 Å2 / Rsym value: 0.092 / Net I/σ(I): 17.9|
|Reflection shell||Resolution: 3.2→3.26 Å / Redundancy: 11.7 % / Mean I/σ(I) obs: 6.8 / Rsym value: 0.457 / % possible all: 95.4|
|Refinement||Method to determine structure: MOLECULAR REPLACEMENT|
Starting model: 2B8W
Resolution: 3.2→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.925 / SU B: 41.573 / SU ML: 0.323 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.478 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
|Solvent computation||Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK|
|Displacement parameters||Biso mean: 60.57 Å2|
|Refinement step||Cycle: LAST / Resolution: 3.2→30 Å|
|Refine LS restraints|
|Refine LS restraints NCS|
Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
|LS refinement shell||Resolution: 3.2→3.26 Å / Total num. of bins used: 27 |
|Refinement TLS params.|
Method: refined / Refine-ID: X-RAY DIFFRACTION
|Refinement TLS group|
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