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Yorodumi- PDB-7sn8: Cryo-EM structure of Drosophila Integrator cleavage module (IntS4... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sn8 | ||||||||||||
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Title | Cryo-EM structure of Drosophila Integrator cleavage module (IntS4-IntS9-IntS11) in complex with IP6 | ||||||||||||
Components |
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Keywords | NUCLEASE / integrator / inositol hexakisphosphate | ||||||||||||
Function / homology | Function and homology information RNA polymerase II transcribes snRNA genes / snRNA processing / integrator complex / snRNA 3'-end processing / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / nucleus / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å | ||||||||||||
Authors | Lin, M. / Tong, L. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Inositol hexakisphosphate is required for Integrator function. Authors: Min-Han Lin / Madeline K Jensen / Nathan D Elrod / Kai-Lieh Huang / Kevin A Welle / Eric J Wagner / Liang Tong / Abstract: Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of ...Integrator is a multi-subunit protein complex associated with RNA polymerase II (Pol II), with critical roles in noncoding RNA 3'-end processing and transcription attenuation of a broad collection of mRNAs. IntS11 is the endonuclease for RNA cleavage, as a part of the IntS4-IntS9-IntS11 Integrator cleavage module (ICM). Here we report a cryo-EM structure of the Drosophila ICM, at 2.74 Å resolution, revealing stable association of an inositol hexakisphosphate (IP) molecule. The IP binding site is located in a highly electropositive pocket at an interface among all three subunits of ICM, 55 Å away from the IntS11 active site and generally conserved in other ICMs. We also confirmed IP association with the same site in human ICM. IP binding is not detected in ICM samples harboring mutations in this binding site. Such mutations or disruption of IP biosynthesis significantly reduced Integrator function in snRNA 3'-end processing and mRNA transcription attenuation. Our structural and functional studies reveal that IP is required for Integrator function in Drosophila, humans, and likely other organisms. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sn8.cif.gz | 303.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sn8.ent.gz | 236.5 KB | Display | PDB format |
PDBx/mmJSON format | 7sn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/7sn8 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/7sn8 | HTTPS FTP |
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-Related structure data
Related structure data | 25214MC 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: 114728.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: IntS4, l(1)G0095, CG12113 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9W3E1 | ||||
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#2: Protein | Mass: 67683.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: IntS11, CG1972 / Production host: Trichoplusia ni (cabbage looper) References: UniProt: Q9VAH9, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters | ||||
#3: Protein | Mass: 73351.531 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: IntS9, CG5222 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q95TS5 | ||||
#4: Chemical | #5: Chemical | ChemComp-IHP / | 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 | Name: Integrator cleavage module with inositol hexakisphosphate Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 51.35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 4395 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 620438 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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