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- EMDB-18149: GBP1 bound by 14-3-3sigma -

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Basic information

Entry
Database: EMDB / ID: EMD-18149
TitleGBP1 bound by 14-3-3sigma
Map data
Sample
  • Complex: GBP1 bound by 14-3-3sigma
    • Protein or peptide: Guanylate-binding protein 1
    • Protein or peptide: 14-3-3 protein sigma
KeywordsProtein complex / Phosphorylation / IMMUNE SYSTEM
Function / homology
Function and homology information


GDP phosphatase activity / non-canonical inflammasome complex assembly / negative regulation of substrate adhesion-dependent cell spreading / protein localization to vacuole / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway ...GDP phosphatase activity / non-canonical inflammasome complex assembly / negative regulation of substrate adhesion-dependent cell spreading / protein localization to vacuole / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / spectrin binding / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / defense response to protozoan / keratinocyte development / keratinization / cytokine binding / regulation of cell-cell adhesion / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / keratinocyte proliferation / cellular response to interleukin-1 / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / negative regulation of protein localization to plasma membrane / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / regulation of protein localization to plasma membrane / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / positive regulation of protein localization / regulation of calcium-mediated signaling / positive regulation of cell adhesion / cytoplasmic vesicle membrane / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / negative regulation of protein kinase activity / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / lipopolysaccharide binding / Hsp90 protein binding / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / intrinsic apoptotic signaling pathway in response to DNA damage / Interferon gamma signaling / GDP binding / intracellular protein localization / cellular response to tumor necrosis factor / actin cytoskeleton / regulation of protein localization / actin binding / G protein activity / positive regulation of cell growth / cytoplasmic vesicle / 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 / protein kinase binding / GTP binding / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / 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, 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. / 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, 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. / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.12 Å
AuthorsPfleiderer MM / Liu X / Fisch D / Anastasakou E / Frickel EM / Galej WP
Funding support Germany, France, European Union, United Kingdom, 9 items
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, 2023-
Header (metadata) releaseOct 11, 2023-
Map releaseOct 11, 2023-
UpdateOct 18, 2023-
Current statusOct 18, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18149.png

Downloads & links

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Map

FileDownload / File: emd_18149.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 600 pix.
= 382.8 Å		0.64 Å/pix.
x 600 pix.
= 382.8 Å		0.64 Å/pix.
x 600 pix.
= 382.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.638 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0402
Minimum - Maximum-0.057743937 - 0.177641
Average (Standard dev.)-0.00032096676 (±0.0032856034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 382.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18149_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18149_half_map_2.map
Projections & Slices
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Sample components

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Entire : GBP1 bound by 14-3-3sigma

EntireName: GBP1 bound by 14-3-3sigma
Components
  • Complex: GBP1 bound by 14-3-3sigma
    • Protein or peptide: Guanylate-binding protein 1
    • Protein or peptide: 14-3-3 protein sigma

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Supramolecule #1: GBP1 bound by 14-3-3sigma

SupramoleculeName: GBP1 bound by 14-3-3sigma / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Guanylate-binding protein 1

MacromoleculeName: Guanylate-binding protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.275539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTGPMCLIEN TNGRLMANPE ALKILSAITQ PMVVVAIVGL YRTGKSYLMN KLAGKKKGFS LGSTVQSHTK GIWMWCVPHP KKPGHILVL LDTEGLGDVE KGDNQNDSWI FALAVLLSST FVYNSIGTIN QQAMDQLYYV TELTHRIRSK SSPDENENEV E DSADFVSF ...String:
MTGPMCLIEN TNGRLMANPE ALKILSAITQ PMVVVAIVGL YRTGKSYLMN KLAGKKKGFS LGSTVQSHTK GIWMWCVPHP KKPGHILVL LDTEGLGDVE KGDNQNDSWI FALAVLLSST FVYNSIGTIN QQAMDQLYYV TELTHRIRSK SSPDENENEV E DSADFVSF FPDFVWTLRD FSLDLEADGQ PLTPDEYLTY SLKLKKGTSQ KDETFNLPRL CIRKFFPKKK CFVFDRPVHR RK LAQLEKL QDEELDPEFV QQVADFCSYI FSNSKTKTLS GGIQVNGPRL ESLVLTYVNA ISSGDLPCME NAVLALAQIE NSA AVQKAI AHYEQQMGQK VQLPTETLQE LLDLHRDSER EAIEVFIRSS FKDVDHLFQK ELAAQLEKKR DDFCKQNQEA SSDR CSALL QVIFSPLEEE VKAGIYSKPG GYRLFVQKLQ DLKKKYYEEP RKGIQAEEIL QTYLKSKESM TDAILQTDQT LTEKE KEIE VERVKAESAQ ASAKMLQEMQ RKNEQMMEQK ERSYQEHLKQ LTEKMENDRV QLLKEQERTL ALKLQEQEQL LKEGFQ KES RIMKNEIQDL QTKM

UniProtKB: Guanylate-binding protein 1

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Macromolecule #2: 14-3-3 protein sigma

MacromoleculeName: 14-3-3 protein sigma / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.139461 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MERASLIQKA KLAEQAERYE DMAAFMKGAV EKGEELSCEE RNLLSVAYKN VVGGQRAAWR VLSSIEQKSN EEGSEEKGPE VREYREKVE TELQGVCDTV LGLLDSHLIK EAGDAESRVF YLKMKGDYYR YLAEVATGDD KKRIIDSARS AYQEAMDISK K EMPPTNPI ...String:
MERASLIQKA KLAEQAERYE DMAAFMKGAV EKGEELSCEE RNLLSVAYKN VVGGQRAAWR VLSSIEQKSN EEGSEEKGPE VREYREKVE TELQGVCDTV LGLLDSHLIK EAGDAESRVF YLKMKGDYYR YLAEVATGDD KKRIIDSARS AYQEAMDISK K EMPPTNPI RLGLALNFSV FHYEIANSPE EAISLAKTTF DEAMADLHTL SEDSYKDSTL IMQLLRDNLT LWT

UniProtKB: 14-3-3 protein sigma

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 7.8
Component:
ConcentrationFormulaName
150.0 mMKClPotassium chloride
20.0 mMHEPES-KOH

Details: 150 mM KCl, 20 mM HEPES-KOH pH 7.8
GridPretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Pressure: 30.0 kPa
Details: Glow discharged for 20 seconds at 25 mA and 0.3 bar using a Pelco EasyGlow device.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 14974 / Average exposure time: 8.0 sec. / Average electron dose: 65.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 420768
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18717
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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