+Open data
-Basic information
Entry | Database: PDB / ID: 7slp | |||||||||||||||
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Title | Cryo-EM structure of 7SK core RNP with linear RNA | |||||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / non-coding RNA / La-related protein / methylphosphate capping enzyme / transcription regulation / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||||||||
Function / homology | Function and homology information RNA 5'-gamma-phosphate methyltransferase activity / U6 2'-O-snRNA methylation / snRNA metabolic process / snRNA modification / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / snRNA binding / positive regulation of protein localization to Cajal body / box C/D sno(s)RNA 3'-end processing ...RNA 5'-gamma-phosphate methyltransferase activity / U6 2'-O-snRNA methylation / snRNA metabolic process / snRNA modification / 7SK snRNP / positive regulation of snRNA transcription by RNA polymerase II / 7SK snRNA binding / snRNA binding / positive regulation of protein localization to Cajal body / box C/D sno(s)RNA 3'-end processing / RNA methyltransferase activity / RNA methylation / negative regulation of viral transcription / S-adenosylmethionine-dependent methyltransferase activity / regulation of mRNA splicing, via spliceosome / O-methyltransferase activity / negative regulation of transcription elongation by RNA polymerase II / positive regulation of G1/S transition of mitotic cell cycle / U6 snRNA binding / RNA splicing / Transferases; Transferring one-carbon groups; Methyltransferases / mRNA processing / spermatogenesis / cell differentiation / ribonucleoprotein complex / mRNA binding / negative regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
Authors | Yang, Y. / Liu, S. / Zhou, Z.H. / Feigon, J. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural basis of RNA conformational switching in the transcriptional regulator 7SK RNP. Authors: Yuan Yang / Shiheng Liu / Sylvain Egloff / Catherine D Eichhorn / Tanya Hadjian / James Zhen / Tamás Kiss / Z Hong Zhou / Juli Feigon / Abstract: 7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is ...7SK non-coding RNA (7SK) negatively regulates RNA polymerase II (RNA Pol II) elongation by inhibiting positive transcription elongation factor b (P-TEFb), and its ribonucleoprotein complex (RNP) is hijacked by HIV-1 for viral transcription and replication. Methylphosphate capping enzyme (MePCE) and La-related protein 7 (Larp7) constitutively associate with 7SK to form a core RNP, while P-TEFb and other proteins dynamically assemble to form different complexes. Here, we present the cryo-EM structures of 7SK core RNP formed with two 7SK conformations, circular and linear, and uncover a common RNA-dependent MePCE-Larp7 complex. Together with NMR, biochemical, and cellular data, these structures reveal the mechanism of MePCE catalytic inactivation in the core RNP, unexpected interactions between Larp7 and RNA that facilitate a role as an RNP chaperone, and that MePCE-7SK-Larp7 core RNP serves as a scaffold for switching between different 7SK conformations essential for RNP assembly and regulation of P-TEFb sequestration and release. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7slp.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7slp.ent.gz | 98 KB | Display | PDB format |
PDBx/mmJSON format | 7slp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7slp_validation.pdf.gz | 1005.1 KB | Display | wwPDB validaton report |
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Full document | 7slp_full_validation.pdf.gz | 1012.5 KB | Display | |
Data in XML | 7slp_validation.xml.gz | 23.1 KB | Display | |
Data in CIF | 7slp_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sl/7slp ftp://data.pdbj.org/pub/pdb/validation_reports/sl/7slp | HTTPS FTP |
-Related structure data
Related structure data | 25197MC 7slqC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 35122.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MEPCE, BCDIN3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q7L2J0, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Protein | Mass: 55109.129 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LARP7, HDCMA18P / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q4G0J3 |
#3: RNA chain | Mass: 26096.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: Chemical | ChemComp-SAH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) / Strain: BL21(DE3) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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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: 130000 X / 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 | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.18rc3_3805: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 159349 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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