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- PDB-9o3z: Phosphonull (T209A) of stress-activating residues -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9o3z
TitlePhosphonull (T209A) of stress-activating residues
Components
  • RsbR
  • RsbT antagonist protein RsbS
KeywordsTRANSCRIPTION / Environmental Stress / Sensor Proteins / Signal Transduction / Effector Response
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsMartinez-Bond, E.A. / Lopez-Ayala, I. / Qiu, L. / Garda, V. / Yu, Z. / Williams, A.H.
Funding support United States, 2items
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 (T209A) of stress-activating residues
Authors: Martinez-Bond, E.A. / Lopez-Ayala, I. / Lobanovska, M. / Qiu, L. / Zhao, Z. / Garda, V. / Yu, Z. / Portnoy, D.A. / Williams, A.H.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RsbR
AB: RsbR
B: RsbR
BB: RsbR
C: RsbR
CB: RsbR
D: RsbR
DB: RsbR
E: RsbR
EB: RsbR
F: RsbR
FB: RsbR
G: RsbR
GB: RsbR
H: RsbR
HB: RsbR
I: RsbR
IB: RsbR
J: RsbR
JB: RsbR
K: RsbR
KB: RsbR
L: RsbR
LB: RsbR
M: RsbR
MB: RsbR
N: RsbR
NB: RsbR
O: RsbR
OB: RsbR
P: RsbR
PB: RsbR
Q: RsbR
QB: RsbR
R: RsbR
RB: RsbR
S: RsbR
SB: RsbR
T: RsbR
TB: RsbR
U: RsbR
UB: RsbR
V: RsbR
VB: RsbR
W: RsbR
WB: RsbR
a: RsbT antagonist protein RsbS
ab: RsbT antagonist protein RsbS
b: RsbT antagonist protein RsbS
bb: RsbT antagonist protein RsbS
c: RsbT antagonist protein RsbS
cb: RsbT antagonist protein RsbS
d: RsbT antagonist protein RsbS
db: RsbT antagonist protein RsbS
e: RsbT antagonist protein RsbS
eb: RsbT antagonist protein RsbS
f: RsbT antagonist protein RsbS
fb: RsbT antagonist protein RsbS
g: RsbT antagonist protein RsbS
gb: RsbT antagonist protein RsbS


Theoretical massNumber of molelcules
Total (without water)1,631,21760
Polymers1,631,21760
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
RsbR / RsbT co-antagonist protein RsbRA / STAS domain-containing protein


Mass: 31624.418 Da / Num. of mol.: 46 / Mutation: T209A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: rsbR, rsbra, A8L61_02205, AB917_06055, ABZ57_01205, AJL21_11595, AJL21_16610, ART25_01260, ARY78_01760, B1N52_01980, B1S26_02045, B5K54_03420, BB997_02140, BCZ21_01050, CA369_02175, CAC64_ ...Gene: rsbR, rsbra, A8L61_02205, AB917_06055, ABZ57_01205, AJL21_11595, AJL21_16610, ART25_01260, ARY78_01760, B1N52_01980, B1S26_02045, B5K54_03420, BB997_02140, BCZ21_01050, CA369_02175, CAC64_11150, CAV64_00900, CW895_01155, D4920_04100, D4B11_12895, D5N24_01410, D7104_06705, DCT16_02105, DQ70_02095, DU018_08835, DYZ80_00353, E1W56_02355, E5F58_02030, E5H26_04030, EX365_01790, EXZ73_11755, F6436_03580, FA835_02005, FC284_05485, FLQ97_01695, FLR03_04330, FNX40_11545, G3O21_000716, GI949_06455, GJW51_01585, GQG13_02275, GYS09_04305, GYX23_13120, GYY14_01065, HQN34_000548, HZJ64_00925, IP987_001914, KV70_05945, QD52_01795, UI29_01810, Y261_01720
Production host: Escherichia coli (E. coli) / References: UniProt: Q8GD19
#2: Protein
RsbT antagonist protein RsbS / STAS domain-containing protein


Mass: 12606.707 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: rsbs, rsbS, A3R20_02220, A8L61_02200, AB917_06050, ABZ57_01200, AE233_01838, AF817_04135, AJL21_11600, AJL21_16615, AP104_09905, APD94_04425, ARR48_04430, ART25_01265, ARY78_01755, B1N52_01975, ...Gene: rsbs, rsbS, A3R20_02220, A8L61_02200, AB917_06050, ABZ57_01200, AE233_01838, AF817_04135, AJL21_11600, AJL21_16615, AP104_09905, APD94_04425, ARR48_04430, ART25_01265, ARY78_01755, B1N52_01975, B1S26_02040, B4X68_06890, B5K54_03415, BB997_02145, BCZ19_01990, BCZ21_01045, BES38_03995, CA369_02170, CAC64_11145, CAV64_00905, CD20_08965, CW845_09085, CW895_01150, D4271_06060, D4920_04105, D4B11_12890, D4C60_07325, D4D89_06750, D4U23_01975, D5M70_11465, D5N24_01415, D7104_06700, DCK61_03360, DCT16_02110, DG57_12350, DOV25_10305, DQ70_02100, DU018_08830, DYZ50_02397, DYZ80_00352, E0I39_06815, E1V33_07140, E1W43_02220, E1W56_02360, E1X78_01785, E5F58_02025, E5H26_04025, EX365_01785, EXZ73_11750, F1788_04060, F6436_03575, F6515_03435, FA835_02010, FC284_05490, FJU19_06655, FLQ97_01690, FLR03_04325, FNX40_11540, FPL45_04955, FV747_04700, FZX01_04925, G3O21_000715, G3R95_001384, GCV64_04085, GHH22_07635, GHO09_07360, GI230_10345, GI949_06450, GIH49_03255, GJW51_01580, GQG13_02280, GT011_04115, GYO01_03260, GYP27_11040, GYR60_01075, GYS09_04300, GYX23_13115, GYY14_01060, GZK27_12030, HQN34_000549, HZJ64_00920, IP987_001913, KV70_05940, QD52_01790, UI29_01805, Y261_01715
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D8X5U2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RsbR(T175A)-RsbS / Type: COMPLEX
Details: Assembled in vitro and purified over Gel filtration
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8.5
Details: 20 mM Tris-HCl pH 8.5, 250 mM NaCl, 1 mM DTT, and 1 mM adenosine 5 diphosphate sodium salt
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 233090 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00358846
ELECTRON MICROSCOPYf_angle_d0.68479668
ELECTRON MICROSCOPYf_dihedral_angle_d4.1948028
ELECTRON MICROSCOPYf_chiral_restr0.04910404
ELECTRON MICROSCOPYf_plane_restr0.0049998

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