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- EMDB-37444: Cryo-EM structure of PAO1-ImcA with GMPCPP -

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Basic information

Entry
Database: EMDB / ID: EMD-37444
TitleCryo-EM structure of PAO1-ImcA with GMPCPP
Map data
Sample
  • Complex: GGDEF domain-containing protein
    • Protein or peptide: Diguanylate cyclase
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsGGDEF domain / diguanylate cyclase activity / membrane protein
Function / homology
Function and homology information


negative regulation of bacterial-type flagellum-dependent cell motility / diguanylate cyclase / diguanylate cyclase activity / cell adhesion involved in single-species biofilm formation / plasma membrane
Similarity search - Function
: / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhan XL / Zhang K / Wang CC / Fan Q / Tang XJ / Zhang X / Wang K / Fu Y / Liang HH
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa.
Authors: Xueliang Zhan / Kuo Zhang / Chenchen Wang / Qiao Fan / Xiujia Tang / Xi Zhang / Ke Wang / Yang Fu / Haihua Liang /
Abstract: Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous ...Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.
History
DepositionSep 13, 2023-
Header (metadata) releaseMar 13, 2024-
Map releaseMar 13, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37444.png

Downloads & links

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Map

FileDownload / File: emd_37444.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 360 pix.
= 240.48 Å		0.67 Å/pix.
x 360 pix.
= 240.48 Å		0.67 Å/pix.
x 360 pix.
= 240.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.668 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.0039323727 - 2.1158953
Average (Standard dev.)0.0017142722 (±0.029541744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 240.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_37444_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_37444_half_map_2.map
Projections & Slices
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Sample components

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Entire : GGDEF domain-containing protein

EntireName: GGDEF domain-containing protein
Components
  • Complex: GGDEF domain-containing protein
    • Protein or peptide: Diguanylate cyclase
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: GGDEF domain-containing protein

SupramoleculeName: GGDEF domain-containing protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Diguanylate cyclase

MacromoleculeName: Diguanylate cyclase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 51.329805 KDa
Recombinant expressionOrganism: Escherichia coli B (bacteria)
SequenceString: MGSDYDIPTT ENLYFQGSML ARDSLVQAGL PDNPYARQLR NGFRWLRFEK ELENEFREFL SWNSLMQRRA AIGVAFLIWA LFIVADWMM VDIRLHPSLF EQLLGVRLGM IGLLLVVWPA AFLPSLRKVG DAIAPYCLLL INLAVLACDV LFEWHGVPRF T QLGATLGI ...String:
MGSDYDIPTT ENLYFQGSML ARDSLVQAGL PDNPYARQLR NGFRWLRFEK ELENEFREFL SWNSLMQRRA AIGVAFLIWA LFIVADWMM VDIRLHPSLF EQLLGVRLGM IGLLLVVWPA AFLPSLRKVG DAIAPYCLLL INLAVLACDV LFEWHGVPRF T QLGATLGI LAVFFPLGLA FWACVRLALL CLALNLAVFL LFGGEENLRT NLLNTLYNGL VVLICSFALY LQDYAQREQF LG RRLLGMM AEQDSLTGLV NRRYYELLAQ RALEQGAREE KGVALILVDV DDFKAYNDHY GHPAGDAALR QLGVVLRQGA RRP LDIAAR LGGEEFAVLL YDSEEGNTLA IAERLRQAVE ALGIEHLGSS AGPCLTISLG VAYSTSGMGL DALYREADRA LYEA KDAGR NAVRVAFRQH DRLEGSFLSA WSHPQFEKGG GSGGGSGGGS WSHPQFEKLE HHHHHH

UniProtKB: diguanylate cyclase

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Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 2 / Number of copies: 4 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205294
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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