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- EMDB-45489: DosP Apo Bent form -

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Basic information

Entry
Database: EMDB / ID: EMD-45489
TitleDosP Apo Bent form
Map data
Sample
  • Complex: DosP apo bent form
    • Protein or peptide: Oxygen sensor protein DosP
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: OXYGEN MOLECULE
KeywordsHeme / DosP / Phosphodiesterase / c-di-GMP / OXYGEN BINDING
Function / homology
Function and homology information


cyclic-guanylate-specific phosphodiesterase / regulation of single-species biofilm formation / cyclic-guanylate-specific phosphodiesterase activity / response to oxygen levels / oxygen sensor activity / heme binding / magnesium ion binding / protein homodimerization activity / plasma membrane
Similarity search - Function
Diguanylate cyclase/phosphodiesterase / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. ...Diguanylate cyclase/phosphodiesterase / : / Putative diguanylate phosphodiesterase / EAL domain / EAL domain superfamily / EAL domain profile. / EAL domain / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / PAC motif / Motif C-terminal to PAS motifs (likely to contribute to PAS structural domain) / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Oxygen sensor protein DosP
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsKumar P / Kober DL
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00 GM141261 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM129547 United States
CitationJournal: Nat Commun / Year: 2024
Title: Structures of the multi-domain oxygen sensor DosP: remote control of a c-di-GMP phosphodiesterase by a regulatory PAS domain.
Authors: Wenbi Wu / Pankaj Kumar / Chad A Brautigam / Shih-Chia Tso / Hamid R Baniasadi / Daniel L Kober / Marie-Alda Gilles-Gonzalez /
Abstract: The heme-based direct oxygen sensor DosP degrades c-di-GMP, a second messenger nearly unique to bacteria. In stationary phase Escherichia coli, DosP is the most abundant c-di-GMP phosphodiesterase. ...The heme-based direct oxygen sensor DosP degrades c-di-GMP, a second messenger nearly unique to bacteria. In stationary phase Escherichia coli, DosP is the most abundant c-di-GMP phosphodiesterase. Ligation of O to a heme-binding PAS domain (hPAS) of the protein enhances the phosphodiesterase through an allosteric mechanism that has remained elusive. We determine six structures of full-length DosP in its aerobic or anaerobic conformations, with or without c-di-GMP. DosP is an elongated dimer with the regulatory heme containing domain and phosphodiesterase separated by nearly 180 Å. In the absence of substrate, regardless of the heme status, DosP presents an equilibrium of two distinct conformations. Binding of substrate induces DosP to adopt a single, ON-state or OFF-state conformation depending on its heme status. Structural and biochemical studies of this multi-domain sensor and its mutants provide insights into signal regulation of second-messenger levels.
History
DepositionJun 25, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45489.png

Downloads & links

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Map

FileDownload / File: emd_45489.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.61 Å/pix.
x 256 pix.
= 413.3 Å		1.61 Å/pix.
x 256 pix.
= 413.3 Å		1.61 Å/pix.
x 256 pix.
= 413.3 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.61445 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.123
Minimum - Maximum-0.22606386 - 0.9851913
Average (Standard dev.)-0.00086201774 (±0.018153634)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 413.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45489_additional_1.map
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Half map: #2

Fileemd_45489_half_map_1.map
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Half map: #1

Fileemd_45489_half_map_2.map
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Sample components

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Entire : DosP apo bent form

EntireName: DosP apo bent form
Components
  • Complex: DosP apo bent form
    • Protein or peptide: Oxygen sensor protein DosP
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: OXYGEN MOLECULE

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Supramolecule #1: DosP apo bent form

SupramoleculeName: DosP apo bent form / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Oxygen sensor protein DosP

MacromoleculeName: Oxygen sensor protein DosP / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: cyclic-guanylate-specific phosphodiesterase
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 91.154109 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRQDAEVIMK LTDADSAADG IFFPALEQNM MGAVLINEND EVMFFNPAAE KLWGYKREEV IGNNIDMLIP RDLRPAHPEY IRHNREGGK ARVEGMSREL QLEKKDGSKI WTRFALSKVS AEGKVYYLAL VRDASVEMAQ KEQTRQLIIA VDHLDRPVIV L DPERHIVQ ...String:
MRQDAEVIMK LTDADSAADG IFFPALEQNM MGAVLINEND EVMFFNPAAE KLWGYKREEV IGNNIDMLIP RDLRPAHPEY IRHNREGGK ARVEGMSREL QLEKKDGSKI WTRFALSKVS AEGKVYYLAL VRDASVEMAQ KEQTRQLIIA VDHLDRPVIV L DPERHIVQ CNRAFTEMFG YCISEASGMQ PDTLLNTPEF PADNRIRLQQ LLWKTARDQD EFLLLTRTGE KIWIKASISP VY DVLAHLQ NLVMTFSDIT EERQIRQLEG NILAAMCSSP PFHEMGEIIC RNIESVLNES HVSLFALRNG MPIHWASSSH GAE IQNAQS WSATIRQRDG APAGILQIKT SSGAETSAFI ERVADISQHM AALALEQEKS RQHIEQLIQF DPMTGLPNRN NLHN YLDDL VDKAVSPVVY LIGVDHIQDV IDSLGYAWAD QALLEVVNRF REKLKPDQYL CRIEGTQFVL VSLENDVSNI TQIAD ELRN VVSKPIMIDD KPFPLTLSIG ISYDLGKNRD YLLSTAHNAM DYIRKNGGNG WQFFSPAMNE MVKERLVLGA ALKEAI SNN QLKLVYQPQI FAETGELYGI EALARWHDPL HGHVPPSRFI PLAEEIGEIE NIGRWVIAEA CRQLAEWRSQ NIHIPAL SV NLSALHFRSN QLPNQVSDAM HAWGIDGHQL TVEITESMMM EHDTEIFKRI QILRDMGVGL SVDDFGTGFS GLSRLVSL P VTEIKIDKSF VDRCLTEKRI LALLEAITSI GQSLNLTVVA EGVETKEQFE MLRKIHCRVI QGYFFSRPLP AEEIPGWMS SVLPLK

UniProtKB: Oxygen sensor protein DosP

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: OXYGEN MOLECULE

MacromoleculeName: OXYGEN MOLECULE / type: ligand / ID: 3 / Number of copies: 2 / Formula: OXY
Molecular weightTheoretical: 31.999 Da
Chemical component information

ChemComp-O2:
OXYGEN MOLECULE

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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
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 80 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154173
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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