SASDEG8: Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), d...

Basic information

• Entry: Database: SASBDB / ID: SASDEG8

Sample

Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), dimer from SEC-SAXS

• 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 T cell receptor signaling pathway / negative regulation of interleukin-2 production / spectrin binding / defense response to protozoan / cytokine binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / negative regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / lipopolysaccharide binding / Hsp90 protein binding / cytoplasmic vesicle membrane / cellular response to type II interferon / G protein activity / negative regulation of ERK1 and ERK2 cascade / Interferon gamma signaling / GDP binding / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 #2219: ; Type: atomic / Chi-square value: ******; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2218: ; Type: atomic / Chi-square value: 6.45; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Human Guanylate Binding Protein 1 with GppNHp (hGBP1 + GppNHp), dimer from SEC-SAXS; Specimen concentration: 55 mg/ml
• Buffer: Name: 50 mM Tris-HCl, 5 mM MgCl2, 150 mM NaCl, 0.2 mM GppNHp; pH: 7.9

Entity #1224

Name: hGBP1 / Type: protein / Description: human Guanylate-binding protein 1 / Formula weight: 69.169 / Num. of mol.: 2 / 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 synchrotron / 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), dimer from SEC-SAXS
Measurement date: Apr 30, 2017 / Storage temperature: 20 °C / Cell temperature: 20 °C / Exposure time: 1 sec. / Number of frames: 3600 / Unit: 1/nm /

	Min	Max
Q	0.0468	4.9445

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 285 /

	Min	Max
Q	0.126936	1.46566
P(R) point	1	285
R	0	22

Result

Type of curve: single_conc /

	Experimental	Porod
MW	159.38 kDa	168.49 kDa
Volume	-	269.6 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	157.4	155.5	0.16
Radius of gyration, Rg	5.728 nm	5.45 nm	0.19

	Min	Max
D	-	22
Guinier point	18	32