SASDEF8: Human Guanylate Binding Protein 1 (hGBP1), monomer from SEC-SAXS

Basic information

• Entry: Database: SASBDB / ID: SASDEF8

Sample

Human Guanylate Binding Protein 1 (hGBP1), monomer from SEC-SAXS

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

Function / homology

Function:

Regulation of GBP-mediated host defense / GBP-mediated host defense / GDP phosphatase activity / non-canonical inflammasome complex assembly / negative regulation of substrate adhesion-dependent cell spreading / CASP4 inflammasome assembly / protein localization to vacuole / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / symbiont cell surface / NS1 Mediated Effects on Host Pathways / vesicle membrane / Enterobacterial factors antagonize host defense / negative regulation of interleukin-2 production / defense response to protozoan / spectrin binding / cytokine binding / cellular response to interleukin-1 / negative regulation of T cell receptor signaling pathway / negative regulation of protein localization to plasma membrane / regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / regulation of calcium-mediated signaling / cytoplasmic vesicle membrane / lipopolysaccharide binding / negative regulation of ERK1 and ERK2 cascade / Hsp90 protein binding / cellular response to type II interferon / cellular response to tumor necrosis factor / Interferon gamma signaling / GDP binding / actin cytoskeleton / actin binding / G protein activity / cytoplasmic vesicle / defense response to virus / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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, C-terminal domain superfamily / Guanylate-binding protein, N-terminal / 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 #2202: ; Type: atomic / Chi-square value: 15.057; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2203: ; Type: atomic / Chi-square value: 1.39; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Human Guanylate Binding Protein 1 (hGBP1), monomer from SEC-SAXS; Specimen concentration: 16 mg/ml
• Buffer: Name: 50 mM Tris-HCl, 5 mM MgCl2, 150 mM NaCl / 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 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 (hGBP1), monomer 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	0.0327	4.9445

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 770 /

	Min	Max
Q	0.174074	3.799
P(R) point	1	770
R	0	13.44

Result

Type of curve: single_conc /

	Experimental	Porod
MW	65.3 kDa	66.08 kDa
Volume	-	105.72 nm3

	P(R)	Guinier	Guinier error
Forward scattering, I0	66.23	65.89	0.057
Radius of gyration, Rg	4.02 nm	3.89 nm	0.06

	Min	Max
D	-	13.44
Guinier point	31	52