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- EMDB-18806: Structural insights into the activation mechanism of antimicrobia... -

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Basic information

Entry
Database: EMDB / ID: EMD-18806
TitleStructural insights into the activation mechanism of antimicrobial GBP1: Membrane-bound GBP1 oligomer
Map data
Sample
  • Complex: Membrane-bound oligomer of human guanylate-binding protein 1 (GBP1)
    • Protein or peptide: Guanylate binding protein 1
  • Ligand: ALUMINUM FLUORIDEAluminium fluoride
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsOligomer / GTPase / Interferon-induced / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


innate immune response / GTPase activity / GTP binding
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)
Methodsubtomogram averaging / cryo EM / Resolution: 26.8 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
DepositionNov 1, 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_18806.png

Downloads & links

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Map

FileDownload / File: emd_18806.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 4.4 Å
Density
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-3.3564606 - 4.932745
Average (Standard dev.)0.00019027192 (±0.3213871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 563.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18806_msk_1.map
Projections & Slices
AxesZYX

Projections

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Half map: #2

Fileemd_18806_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18806_half_map_2.map
Projections & Slices
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Sample components

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Entire : Membrane-bound oligomer of human guanylate-binding protein 1 (GBP1)

EntireName: Membrane-bound oligomer of human guanylate-binding protein 1 (GBP1)
Components
  • Complex: Membrane-bound oligomer of human guanylate-binding protein 1 (GBP1)
    • Protein or peptide: Guanylate binding protein 1
  • Ligand: ALUMINUM FLUORIDEAluminium fluoride
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Membrane-bound oligomer of human guanylate-binding protein 1 (GBP1)

SupramoleculeName: Membrane-bound oligomer of human guanylate-binding protein 1 (GBP1)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / 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 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 69.26793 KDa
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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Macromolecule #2: ALUMINUM FLUORIDE

MacromoleculeName: ALUMINUM FLUORIDE / type: ligand / ID: 2 / Number of copies: 6 / Formula: AF3
Molecular weightTheoretical: 83.977 Da
Chemical component information

ChemComp-AF3:
ALUMINUM FLUORIDE / Aluminium fluoride

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 6 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.68 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 2.8 e/Å2
Details: Tilt series were acquired with a Hybrid-STA (Sanchez et al. 2020, Nat Commun): exposure dose of 2.8 e-/A2 for non-zero tilted projection and 14.4 e-/A2 for zero tilted projection
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 104 / Number images used: 70160
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 26.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 6146
FSC plot (resolution estimation)

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