[English] 日本語
Yorodumi- PDB-7qv9: CryoEM structure of bacterial transcription intermediate complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qv9 | ||||||
---|---|---|---|---|---|---|---|
Title | CryoEM structure of bacterial transcription intermediate complex mediated by activator PspF | ||||||
Components |
| ||||||
Keywords | TRANSCRIPTION / RNA polymerase / AAA protein / transcription regulation / cryoEM | ||||||
Function / homology | Function and homology information DNA-binding transcription activator activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility ...DNA-binding transcription activator activity / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / DNA-directed RNA polymerase complex / nucleotidyltransferase activity / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA-templated transcription initiation / transcription antitermination / cell motility / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) Klebsiella pneumoniae (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Ye, F.Z. / Zhang, X.D. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Sci Adv / Year: 2022 Title: Mechanisms of DNA opening revealed in AAA+ transcription complex structures. Authors: Fuzhou Ye / Forson Gao / Xiaojiao Liu / Martin Buck / Xiaodong Zhang / Abstract: Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter ...Gene transcription is carried out by RNA polymerase (RNAP) and requires the conversion of the initial closed promoter complex, where DNA is double stranded, to a transcription-competent open promoter complex, where DNA is opened up. In bacteria, RNAP relies on σ factors for its promoter specificities. Using a special form of sigma factor (σ), which forms a stable closed complex and requires its activator that belongs to the AAA+ ATPases (ATPases associated with diverse cellular activities), we obtained cryo-electron microscopy structures of transcription initiation complexes that reveal a previously unidentified process of DNA melting opening. The σ amino terminus threads through the locally opened up DNA and then becomes enclosed by the AAA+ hexameric ring in the activator-bound intermediate complex. Our structures suggest how ATP hydrolysis by the AAA+ activator could remove the σ inhibition while helping to open up DNA, using σ amino-terminal peptide as a pry bar. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qv9.cif.gz | 1008.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qv9.ent.gz | 798.4 KB | Display | PDB format |
PDBx/mmJSON format | 7qv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qv9_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qv9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7qv9_validation.xml.gz | 133.1 KB | Display | |
Data in CIF | 7qv9_validation.cif.gz | 207.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/7qv9 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/7qv9 | HTTPS FTP |
-Related structure data
Related structure data | 14171MC 7qwpC 7qxiC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE
#1: Protein | Mass: 36558.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpoA, pez, phs, sez, b3295, JW3257 / Plasmid: pGEXABC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli / References: UniProt: P0A7Z4, DNA-directed RNA polymerase #2: Protein | | Mass: 150820.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 Gene: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950 Plasmid: pGEXABC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli / References: UniProt: P0A8V2, DNA-directed RNA polymerase #3: Protein | | Mass: 155366.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpoC, tabB, b3988, JW3951 / Plasmid: pGEXABC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli / References: UniProt: P0A8T7, DNA-directed RNA polymerase #4: Protein | | Mass: 10249.547 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: rpoZ, b3649, JW3624 / Plasmid: pGEXABC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli / References: UniProt: P0A800, DNA-directed RNA polymerase |
---|
-DNA chain , 2 types, 2 molecules NT
#5: DNA chain | Mass: 19439.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria) |
---|---|
#6: DNA chain | Mass: 19404.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Klebsiella pneumoniae (bacteria) |
-Protein , 2 types, 7 molecules abcdfeM
#7: Protein | Mass: 33187.777 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: pspF / Plasmid: pET28b-PspF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Escherichia coli #8: Protein | | Mass: 53978.656 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: MGSSHHHHHHSSGLVPRGSHMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQTDLHDEVEAKEVEDRESLDTVDALEQKEMPD ELPLDASWDEIYTAGTPSGNGVDYQDDELPVYQGETTQTLQDYLMWQVELTPFTDTDRAIATSIVDAVDDTGYLTIQIED ...Details: MGSSHHHHHHSSGLVPRGSHMKQGLQLRLSQQLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQTDLHDEVEAKEVEDRESLDTVDALEQKEMPD ELPLDASWDEIYTAGTPSGNGVDYQDDELPVYQGETTQTLQDYLMWQVELTPFTDTDRAIATSIVDAVDDTGYLTIQIED IVDSIGDDEIGLEEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFAKETPWLEEARLIISDHLDLLANHDFRTLMRVTR LKEEVLKEAVNLIQSLDPRPGQSIQTSEPEYVIPDVLVRKVSGRWTVELNADSIPRLKINQQYAAMGNSARNDADGQFIR SNLQEARWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIAQAVEMHESTISRVTTQKYLHSPRGIFELK YFFSSHVNTEGGGEASSTAIRALVKKLIAAENPAKPLSDSKLTSMLSEQGIMVARRTVAKYRESLSIPPSNQRKQLV Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: rpoN, A7B01_01570, B4U61_10775, B5L96_24890, BANRA_03272, BL124_00020515, BN49_0508, BS595_02095, C3F39_17700, DDJ63_09965, DRB11_15360, EAO17_11045, FXN67_08250, G5637_17550, G7Z27_02650, ...Gene: rpoN, A7B01_01570, B4U61_10775, B5L96_24890, BANRA_03272, BL124_00020515, BN49_0508, BS595_02095, C3F39_17700, DDJ63_09965, DRB11_15360, EAO17_11045, FXN67_08250, G5637_17550, G7Z27_02650, GJJ08_002620, GJJ12_002565, GNE24_14685, GNG14_08115, GPZ86_02700, HV479_13895, NCTC13465_03419, NCTC3279_03959, NCTC5047_03164, SAMEA3499874_03190, SAMEA3499901_03507, SAMEA3500057_00079, SAMEA3512100_03793, SAMEA3538828_04129, SAMEA3649733_03935, SAMEA3649758_00080, SAMEA3720909_03353, SAMEA3727630_04208, SAMEA3727643_03388, SAMEA3727679_00080, SAMEA3729663_03804, SAMEA4364603_00630, SAMEA4873632_04262 Plasmid: pET28b-sigma54 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Escherichia coli BL21(DE3 / References: UniProt: A0A0N9UTC1 |
---|
-Non-polymers , 2 types, 9 molecules
#9: Chemical | ChemComp-ADP / #10: Chemical | ChemComp-AF3 / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Bacterial transcription intermediate complex mediated by PspF activator protein Type: COMPLEX / Entity ID: #1-#8 / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.71 MDa / Experimental value: NO | |||||||||||||||||||||||||
Buffer solution | pH: 8 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1400 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.1 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14780 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 2000000 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33285 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5NSS Accession code: 5NSS / Source name: PDB / Type: experimental model |