SASDEM8: Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), b...

Basic information

• Entry: Database: SASBDB / ID: SASDEM8

Sample

Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), batch mode

• human Guanylate-binding protein 1 (protein), hGBP1, Homo sapiens

Function / homology

Function:

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 / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / 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 / cytosol / cytoplasm

Domain/homology:

Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase

Component:

Guanylate-binding protein 1

• Biological species: Homo sapiens (human)
• Citation: Journal: FEBS J / Year: 2020; Title: Farnesylation of human guanylate-binding protein 1 as safety mechanism preventing structural rearrangements and uninduced dimerization.; Authors: Charlotte Lorenz / Semra Ince / Tao Zhang / Anneliese Cousin / Renu Batra-Safferling / Luitgard Nagel-Steger / Christian Herrmann / Andreas M Stadler / ; Abstract: Human guanylate-binding protein 1 (hGBP1) belongs to the family of dynamin-like proteins and is activated by addition of nucleotides, leading to protein oligomerization and stimulated GTPase activity. In vivo, hGBP1 is post-translationally modified by attachment of a farnesyl group yielding farn-hGBP1. In this study, hydrodynamic differences in farn-hGBP1 and unmodified hGBP1 were investigated using dynamic light scattering (DLS), analytical ultracentrifugation (AUC) and analytical size-exclusion chromatography (SEC). In addition, we performed small-angle X-ray scattering (SAXS) experiments coupled with a SEC setup (SEC-SAXS) to investigate structural properties of nonmodified hGBP1 and farn-hGBP1 in solution. SEC-SAXS measurements revealed that farnesylation keeps hGBP1 in its inactive monomeric and crystal-like conformation in nucleotide-free solution, whereas unmodified hGBP1 forms a monomer-dimer equilibrium both in the inactive ground state in nucleotide-free solution as well as in the activated state that is trapped by addition of the nonhydrolysable GTP analogue GppNHp. Nonmodified hGBP1 is structurally perturbed as compared to farn-hGBP. In particular, GppNHp binding leads to large structural rearrangements and higher conformational flexibility of the monomer and the dimer. Structural changes observed in the nonmodified protein are prerequisites for further oligomer assemblies of farn-hGBP1 that occur in the presence of nucleotides. DATABASE: All SEC-SAXS data, corresponding fits to the data and structural models are deposited in the Small Angle Scattering Biological Data Bank [SASBDB (Nucleic Acids Res, 43, 2015, D357)] with project IDs: SASDEE8, SASDEF8, SASDEG8, SASDEH8, SASDEJ8, SASDEK8, SASDEL8 and SASDEM8.

Contact author

• Charlotte Lorenz (Forschungszentrum Jülich, Germany)

Models

• Model #2214: ; Type: atomic / Chi-square value: ******; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2216: ; Type: atomic / Chi-square value: 35.141; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), batch mode; Specimen concentration: 4 mg/ml
• Buffer: Name: 50 mM Tris-HCl, 5 mM MgCl2, 150 mM NaCl, 0.2 mM GppNHp; pH: 7.9

Entity #1223

Name: hGBP1 / Type: protein / Description: human Guanylate-binding protein 1 / Formula weight: 69.169 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P32455
Sequence:

MRGSHHHHHH GSASEIHMTG PMCLIENTNG RLMANPEALK ILSAITQPMV VVAIVGLYRT GKSYLMNKLA GKKKGFSLGS TVQSHTKGIW MWCVPHPKKP GHILVLLDTE GLGDVEKGDN QNDSWIFALA VLLSSTFVYN SIGTINQQAM DQLYYVTELT HRIRSKSSPD ENENEVEDSA DFVSFFPDFV WTLRDFSLDL EADGQPLTPD EYLTYSLKLK KGTSQKDETF NLPRLCIRKF FPKKKCFVFD RPVHRRKLAQ LEKLQDEELD PEFVQQVADF CSYIFSNSKT KTLSGGIQVN GPRLESLVLT YVNAISSGDL PCMENAVLAL AQIENSAAVQ KAIAHYEQQM GQKVQLPTES LQELLDLHRD SEREAIEVFI RSSFKDVDHL FQKELAAQLE KKRDDFCKQN QEASSDRCSG LLQVIFSPLE EEVKAGIYSK PGGYRLFVQK LQDLKKKYYE EPRKGIQAEE ILQTYLKSKE SMTDAILQTD QTLTEKEKEI EVERVKAESA QASAKMLQEM QRKNEQMMEQ KERSYQEHLK QLTEKMENDR VQLLKEQERT LALKLQEQEQ LLKEGFQKES RIMKNEIQDL QTKMRRRKAC TIS

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.09919 Å / Dist. spec. to detc.: 2.867 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), batch mode
Measurement date: May 8, 2016 / Storage temperature: 22 °C / Cell temperature: 22 °C / Exposure time: 3 sec. / Number of frames: 10 / Unit: 1/A /

	Min	Max
Q	0.0033	0.4946

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 391 /

	Min	Max
Q	0.00750463	0.191403
P(R) point	1	391
R	0	270

Result

Type of curve: single_conc

	Experimental	Standard	Standard error	Porod
MW	109.81 kDa	109.81 kDa	0.21	116 kDa
Volume	-	-	-	186 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	111	109.81	0.21
Radius of gyration, Rg	5.84 nm	5.46 nm	0.27

	Min	Max
D	-	27
Guinier point	6	32