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- EMDB-70101: Phosphomimetic (T209E) of stress-activating residues -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70101
TitlePhosphomimetic (T209E) of stress-activating residues
Map dataT209E
Sample
  • Complex: RsbR(T209E)-RsbS
    • Protein or peptide: RsbR
    • Protein or peptide: RsbT antagonist protein RsbS
KeywordsEnvironmental Stress / Sensor Proteins / Signal Transduction / Effector Response / TRANSCRIPTION
Function / homology
Function and homology information


oxygen binding / heme binding
Similarity search - Function
RsbS co-antagonist protein RsbRA N-terminal domain / Rsbr N terminal / : / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / Globin/Protoglobin
Similarity search - Domain/homology
RsbT antagonist protein RsbS / RsbR
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.02 Å
AuthorsMartinez-Bond EA / Lopez-Ayala I / Qiu L / Garda V / Yu Z / Williams AH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS1R01GM144694 United States
Chan Zuckerberg Initiative7030219 United States
CitationJournal: To Be Published
Title: Phosphonull (T175A) of stress-activating residues
Authors: Martinez-Bond EA / Lopez-Ayala I / Lobanovska M / Qiu L / Zhao Z / Garda V / Yu Z / Portnoy DA / Williams AH
History
DepositionApr 8, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70101.png

Downloads & links

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Map

FileDownload / File: emd_70101.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT209E
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 600 pix.
= 501. Å		0.84 Å/pix.
x 600 pix.
= 501. Å		0.84 Å/pix.
x 600 pix.
= 501. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.835 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.35542393 - 0.9860571
Average (Standard dev.)0.0015320416 (±0.040808998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 501.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: T209E

Fileemd_70101_half_map_1.map
AnnotationT209E
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: T209E

Fileemd_70101_half_map_2.map
AnnotationT209E
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RsbR(T209E)-RsbS

EntireName: RsbR(T209E)-RsbS
Components
  • Complex: RsbR(T209E)-RsbS
    • Protein or peptide: RsbR
    • Protein or peptide: RsbT antagonist protein RsbS

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Supramolecule #1: RsbR(T209E)-RsbS

SupramoleculeName: RsbR(T209E)-RsbS / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Assembled in vitro and purified over Gel filtration
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 1.8 MDa

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Macromolecule #1: RsbR

MacromoleculeName: RsbR / type: protein_or_peptide / ID: 1 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 31.682453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYKDFANFIR TNKADLLNDW MNEMEKQSDQ LINDIAKEAM YEETSKEFVD LIVSNVTENG SKFNEKLDDF AEKVVHLGWP IHFVTTGLR VFGLLVYTAM RDEDLFLKRE EKPEDDAYYR FETWLSSMYN KVVTAYADTW EKTVSIQKSA LQELSAPLLP I FEKISVMP ...String:
MYKDFANFIR TNKADLLNDW MNEMEKQSDQ LINDIAKEAM YEETSKEFVD LIVSNVTENG SKFNEKLDDF AEKVVHLGWP IHFVTTGLR VFGLLVYTAM RDEDLFLKRE EKPEDDAYYR FETWLSSMYN KVVTAYADTW EKTVSIQKSA LQELSAPLLP I FEKISVMP LIGTIDTERA KLIIENLLIG VVKNRSEVVL IDITGVPVVD EMVAHHIIQA SEAVRLVGCQ AMLVGIRPEI AQ TIVNLGI ELDQIITTNT MKKGMERALA LTNREIVEKE G

UniProtKB: RsbR

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Macromolecule #2: RsbT antagonist protein RsbS

MacromoleculeName: RsbT antagonist protein RsbS / type: protein_or_peptide / ID: 2 / Number of copies: 30 / Enantiomer: LEVO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Molecular weightTheoretical: 12.606707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGIPILKLGE CLLISIQSEL DDHTAVEFQE DLLAKIHETS ARGVVIDITS IDFIDSFIAK ILGDVVSMSK LMGAKVVVTG IQPAVAITL IELGITFSGV LSAMDLESGL EKLKQELGE

UniProtKB: RsbT antagonist protein RsbS

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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: 8.5
Details: 20 mM Tris-HCl pH 8.5, 250 mM NaCl, 1 mM DTT, and 1 mM adenosine 5 diphosphate sodium salt
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 31771
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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