[English] 日本語
Yorodumi
- EMDB-18698: Structural insights into the activation mechanism of antimicrobia... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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 / 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 / defense response to protozoan / cytokine binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / cellular response to interleukin-1 / negative regulation of protein localization to plasma membrane / regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / cytoplasmic vesicle membrane / lipopolysaccharide binding / Hsp90 protein binding / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / Interferon gamma signaling / GDP binding / cellular response to tumor necrosis factor / actin cytoskeleton / actin binding / G protein activity / 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 / enzyme binding / Golgi apparatus / 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, 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
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

-
Structure visualization

Supplemental images

emd_18698.png

Downloads & links

-
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
Contrast
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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 °

-
Supplemental data

-
Half map: #2

Fileemd_18698_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18698_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
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

+
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more