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Yorodumi- EMDB-31403: Cryo-EM structure of Pseudomonas aeruginosa SutA transcription ac... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31403 | |||||||||
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Title | Cryo-EM structure of Pseudomonas aeruginosa SutA transcription activation complex | |||||||||
Map data | ||||||||||
Sample |
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Keywords | transcription initiation / Pseudomonas aeruginosa / SutA / transcription activation / sigmaS / RNA polymerase / RNAP beta lobe / TRANSLATION / TRANSCRIPTION-DNA complex | |||||||||
Function / homology | Function and homology information regulation of response to salt stress / negative regulation of secondary metabolite biosynthetic process / positive regulation of single-species biofilm formation on inanimate substrate / regulation of cellular response to oxidative stress / positive regulation of chemotaxis / regulation of cell motility / sigma factor activity / DNA-directed RNA polymerase complex / regulation of cellular response to heat / DNA-templated transcription initiation ...regulation of response to salt stress / negative regulation of secondary metabolite biosynthetic process / positive regulation of single-species biofilm formation on inanimate substrate / regulation of cellular response to oxidative stress / positive regulation of chemotaxis / regulation of cell motility / sigma factor activity / DNA-directed RNA polymerase complex / regulation of cellular response to heat / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) / Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | He DW / You LL | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Pseudomonas aeruginosa SutA wedges RNAP lobe domain open to facilitate promoter DNA unwinding. Authors: Dingwei He / Linlin You / Xiaoxian Wu / Jing Shi / Aijia Wen / Zhi Yan / Wenhui Mu / Chengli Fang / Yu Feng / Yu Zhang / Abstract: Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme ...Pseudomonas aeruginosa (Pae) SutA adapts bacteria to hypoxia and nutrition-limited environment during chronic infection by increasing transcription activity of an RNA polymerase (RNAP) holoenzyme comprising the stress-responsive σ factor σ (RNAP-σ). SutA shows no homology to previously characterized RNAP-binding proteins. The structure and mode of action of SutA remain unclear. Here we determined cryo-EM structures of Pae RNAP-σ holoenzyme, Pae RNAP-σ holoenzyme complexed with SutA, and Pae RNAP-σ transcription initiation complex comprising SutA. The structures show SutA pinches RNAP-β protrusion and facilitates promoter unwinding by wedging RNAP-β lobe open. Our results demonstrate that SutA clears an energetic barrier to facilitate promoter unwinding of RNAP-σ holoenzyme. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_31403.map.gz | 8.9 MB | EMDB map data format | |
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Header (meta data) | emd-31403-v30.xml emd-31403.xml | 26.7 KB 26.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_31403_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_31403.png | 99.1 KB | ||
Masks | emd_31403_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-31403.cif.gz | 8.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31403 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31403 | HTTPS FTP |
-Validation report
Summary document | emd_31403_validation.pdf.gz | 412.9 KB | Display | EMDB validaton report |
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Full document | emd_31403_full_validation.pdf.gz | 412.5 KB | Display | |
Data in XML | emd_31403_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | emd_31403_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31403 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31403 | HTTPS FTP |
-Related structure data
Related structure data | 7f0rMC 7vf9C 7xl3C 7xl4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31403.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_31403_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pseudomonas aeruginosa SutA transcription activation complex
+Supramolecule #1: Pseudomonas aeruginosa SutA transcription activation complex
+Supramolecule #2: Pseudomonas aeruginosa SutA transcription activation
+Supramolecule #3: DNA
+Macromolecule #1: DNA-directed RNA polymerase subunit alpha
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase subunit beta'
+Macromolecule #4: DNA-directed RNA polymerase subunit omega
+Macromolecule #5: Transcriptional factor SutA
+Macromolecule #6: RNA polymerase sigma factor RpoS
+Macromolecule #7: DNA (70-MER)
+Macromolecule #8: DNA (70-MER)
+Macromolecule #9: ZINC ION
+Macromolecule #10: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 13 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 4 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.0 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 22500 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |