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- PDB-8q4l: GBP1 bound by 14-3-3sigma -

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Basic information

Entry
Database: PDB / ID: 8q4l
TitleGBP1 bound by 14-3-3sigma
Components
  • 14-3-3 protein sigma
  • Guanylate-binding protein 1
KeywordsIMMUNE SYSTEM / Protein complex / Phosphorylation
Function / homology
Function and homology information


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 ...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 / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / defense response to protozoan / cytokine binding / regulation of cell-cell adhesion / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / cellular response to interleukin-1 / phosphoserine residue binding / negative regulation of keratinocyte proliferation / Activation of BAD and translocation to mitochondria / regulation of protein localization to plasma membrane / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / positive regulation of protein localization / RHO GTPases activate PKNs / regulation of calcium-mediated signaling / negative regulation of innate immune response / protein sequestering activity / protein kinase A signaling / protein export from nucleus / positive regulation of cell adhesion / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / lipopolysaccharide binding / negative regulation of protein kinase activity / Hsp90 protein binding / cytoplasmic vesicle membrane / cellular response to type II interferon / G protein activity / negative regulation of ERK1 and ERK2 cascade / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon gamma signaling / GDP binding / protein localization / actin cytoskeleton / cellular response to tumor necrosis factor / regulation of protein localization / actin binding / cytoplasmic vesicle / positive regulation of cell growth / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / defense response to virus / regulation of cell cycle / defense response to bacterium / cadherin binding / Golgi membrane / innate immune response / GTPase activity / GTP binding / protein kinase binding / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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. / 14-3-3 protein sigma / 14-3-3 proteins signature 2. ...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. / 14-3-3 protein sigma / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
14-3-3 protein sigma / Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.12 Å
AuthorsPfleiderer, M.M. / Liu, X. / Fisch, D. / Anastasakou, E. / Frickel, E.M. / Galej, W.P.
Funding support Germany, France, European Union, United Kingdom, 9items
OrganizationGrant numberCountry
Boehringer Ingelheim Fonds (BIF) Germany
Human Frontier Science Program (HFSP)LT0006/2022-L France
European Molecular Biology Organization (EMBO)ALTF 491-2022European Union
Wellcome Trust217202/Z/19/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V030930/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/T029323/1 United Kingdom
Wellcome TrustFC001076 United Kingdom
Medical Research Council (MRC, United Kingdom)FC001076 United Kingdom
Cancer Research UKFC001076 United Kingdom
CitationJournal: Science / Year: 2023
Title: PIM1 controls GBP1 activity to limit self-damage and to guard against pathogen infection.
Authors: Daniel Fisch / Moritz M Pfleiderer / Eleni Anastasakou / Gillian M Mackie / Fabian Wendt / Xiangyang Liu / Barbara Clough / Samuel Lara-Reyna / Vesela Encheva / Ambrosius P Snijders / ...Authors: Daniel Fisch / Moritz M Pfleiderer / Eleni Anastasakou / Gillian M Mackie / Fabian Wendt / Xiangyang Liu / Barbara Clough / Samuel Lara-Reyna / Vesela Encheva / Ambrosius P Snijders / Hironori Bando / Masahiro Yamamoto / Andrew D Beggs / Jason Mercer / Avinash R Shenoy / Bernd Wollscheid / Kendle M Maslowski / Wojtek P Galej / Eva-Maria Frickel /
Abstract: Disruption of cellular activities by pathogen virulence factors can trigger innate immune responses. Interferon-γ (IFN-γ)-inducible antimicrobial factors, such as the guanylate binding proteins ...Disruption of cellular activities by pathogen virulence factors can trigger innate immune responses. Interferon-γ (IFN-γ)-inducible antimicrobial factors, such as the guanylate binding proteins (GBPs), promote cell-intrinsic defense by attacking intracellular pathogens and by inducing programmed cell death. Working in human macrophages, we discovered that GBP1 expression in the absence of IFN-γ killed the cells and induced Golgi fragmentation. IFN-γ exposure improved macrophage survival through the activity of the kinase PIM1. PIM1 phosphorylated GBP1, leading to its sequestration by 14-3-3σ, which thereby prevented GBP1 membrane association. During infection, the virulence protein TgIST interfered with IFN-γ signaling and depleted PIM1, thereby increasing GBP1 activity. Although infected cells can restrain pathogens in a GBP1-dependent manner, this mechanism can protect uninfected bystander cells. Thus, PIM1 can provide a bait for pathogen virulence factors, guarding the integrity of IFN-γ signaling.
History
DepositionAug 7, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate-binding protein 1
B: 14-3-3 protein sigma
C: 14-3-3 protein sigma


Theoretical massNumber of molelcules
Total (without water)118,5543
Polymers118,5543
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Guanylate-binding protein 1


Mass: 66275.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P32455
#2: Protein 14-3-3 protein sigma


Mass: 26139.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN / Production host: Escherichia coli (E. coli) / References: UniProt: P31947

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GBP1 bound by 14-3-3sigma / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.12 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.8 / Details: 150 mM KCl, 20 mM HEPES-KOH pH 7.8
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMPotassium chlorideKCl1
220 mMHEPES-KOH1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Glow discharged for 20 seconds at 25 mA and 0.3 bar using a Pelco EasyGlow device.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 8 sec. / Electron dose: 65.5 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14974
Image scansMovie frames/image: 40

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Processing

EM software
IDNameCategory
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 420768
3D reconstructionResolution: 5.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 18717 / Symmetry type: POINT

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