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- EMDB-18698: Structural insights into the activation mechanism of antimicrobia... -

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Entry
Database: EMDB / ID: EMD-18698
TitleStructural insights into the activation mechanism of antimicrobial GBP1: Polymeric assembly of GBP1
Map dataGuanylate-binding protein 1 polymer
Sample
  • Complex: Polymeric assembly of human guanylate-binding protein 1 (GBP1)
    • Protein or peptide: Guanylate-binding protein 1
KeywordsOligomer / GTPase / Interferon-induced / ANTIMICROBIAL PROTEIN
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 / 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 / G protein activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / 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
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. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Guanylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 37.0 Å
AuthorsWeismehl M / Chu X / Kutsch M / Lauterjung P / Herrmann C / Kudryashev M / Daumke O
Funding support Germany, 2 items
OrganizationGrant numberCountry
Helmholtz Association Germany
German Research Foundation (DFG)INST 335/588-1 FUGG Germany
CitationJournal: EMBO J / Year: 2024
Title: Structural insights into the activation mechanism of antimicrobial GBP1.
Authors: Marius Weismehl / Xiaofeng Chu / Miriam Kutsch / Paul Lauterjung / Christian Herrmann / Misha Kudryashev / Oliver Daumke /
Abstract: The dynamin-related human guanylate-binding protein 1 (GBP1) mediates host defenses against microbial pathogens. Upon GTP binding and hydrolysis, auto-inhibited GBP1 monomers dimerize and assemble ...The dynamin-related human guanylate-binding protein 1 (GBP1) mediates host defenses against microbial pathogens. Upon GTP binding and hydrolysis, auto-inhibited GBP1 monomers dimerize and assemble into soluble and membrane-bound oligomers, which are crucial for innate immune responses. How higher-order GBP1 oligomers are built from dimers, and how assembly is coordinated with nucleotide-dependent conformational changes, has remained elusive. Here, we present cryo-electron microscopy-based structural data of soluble and membrane-bound GBP1 oligomers, which show that GBP1 assembles in an outstretched dimeric conformation. We identify a surface-exposed helix in the large GTPase domain that contributes to the oligomerization interface, and we probe its nucleotide- and dimerization-dependent movements that facilitate the formation of an antimicrobial protein coat on a gram-negative bacterial pathogen. Our results reveal a sophisticated activation mechanism for GBP1, in which nucleotide-dependent structural changes coordinate dimerization, oligomerization, and membrane binding to allow encapsulation of pathogens within an antimicrobial protein coat.
History
DepositionOct 20, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18698.png

Downloads & links

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Map

FileDownload / File: emd_18698.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGuanylate-binding protein 1 polymer
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 256 pix.
= 1085.44 Å		4.24 Å/pix.
x 256 pix.
= 1085.44 Å		4.24 Å/pix.
x 256 pix.
= 1085.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.04451926 - 0.13189933
Average (Standard dev.)0.0008361432 (±0.0082212705)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 1085.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_18698_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_18698_half_map_2.map
Projections & Slices
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Sample components

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Entire : Polymeric assembly of human guanylate-binding protein 1 (GBP1)

EntireName: Polymeric assembly of human guanylate-binding protein 1 (GBP1)
Components
  • Complex: Polymeric assembly of human guanylate-binding protein 1 (GBP1)
    • Protein or peptide: Guanylate-binding protein 1

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Supramolecule #1: Polymeric assembly of human guanylate-binding protein 1 (GBP1)

SupramoleculeName: Polymeric assembly of human guanylate-binding protein 1 (GBP1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in complex with GDP-AlFx
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Guanylate-binding protein 1

MacromoleculeName: Guanylate-binding protein 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRGSHHHHHH GSASEIHMTG PMCLIENTNG RLMANPEALK ILSAITQPMV VVAIVGLYRT GKSYLMNKLA GKKKGFSLGS TVQSHTKGI WMWCVPHPKK PGHILVLLDT EGLGDVEKGD NQNDSWIFAL AVLLSSTFVY NSIGTINQQA MDQLYYVTEL T HRIRSKSS ...String:
MRGSHHHHHH GSASEIHMTG PMCLIENTNG RLMANPEALK ILSAITQPMV VVAIVGLYRT GKSYLMNKLA GKKKGFSLGS TVQSHTKGI WMWCVPHPKK PGHILVLLDT EGLGDVEKGD NQNDSWIFAL AVLLSSTFVY NSIGTINQQA MDQLYYVTEL T HRIRSKSS PDENENEVED SADFVSFFPD FVWTLRDFSL DLEADGQPLT PDEYLTYSLK LKKGTSQKDE TFNLPRLCIR KF FPKKKCF VFDRPVHRRK LAQLEKLQDE ELDPEFVQQV ADFCSYIFSN SKTKTLSGGI QVNGPRLESL VLTYVNAISS GDL PCMENA VLALAQIENS AAVQKAIAHY EQQMGQKVQL PTESLQELLD LHRDSEREAI EVFIRSSFKD VDHLFQKELA AQLE KKRDD FCKQNQEASS DRCSGLLQVI FSPLEEEVKA GIYSKPGGYR LFVQKLQDLK KKYYEEPRKG IQAEEILQTY LKSKE SMTD AILQTDQTLT EKEKEIEVER VKAESAQASA KMLQEMQRKN EQMMEQKERS YQEHLKQLTE KMENDRVQLL KEQERT LAL KLQEQEQLLK EGFQKESRIM KNEIQDLQTK MRRRKACTIS

UniProtKB: Guanylate-binding protein 1

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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

Concentration0.35 mg/mL
BufferpH: 7.9
Details: 50 mM Tris-HCl, 150 mM NaCl, 5 mM MgCl2 (supplemented with 200 uM GDP, 300 uM AlCl3, 10 mM NaF)
VitrificationCryogen name: ETHANE
Detailsin complex with GDP-AlFx

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 15952
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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