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Yorodumi- PDB-6dnh: Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dnh | |||||||||
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Title | Cryo-EM structure of human CPSF-160-WDR33-CPSF-30-PAS RNA complex at 3.4 A resolution | |||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Recognition of the AAUAAA polyadenylation signal (PAS) / Hoogsteen base pair / zinc finger / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | Function and homology information co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / mRNA 3'-end processing / postreplication repair ...co-transcriptional RNA 3'-end processing, cleavage and polyadenylation pathway / Inhibition of Host mRNA Processing and RNA Silencing / Processing of Intronless Pre-mRNAs / mRNA cleavage and polyadenylation specificity factor complex / collagen trimer / mRNA 3'-UTR AU-rich region binding / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA 3'-end processing / mRNA 3'-end processing / postreplication repair / tRNA processing in the nucleus / RNA Polymerase II Transcription Termination / Processing of Capped Intron-Containing Pre-mRNA / fibrillar center / mRNA processing / sequence-specific double-stranded DNA binding / spermatogenesis / intracellular membrane-bounded organelle / enzyme binding / RNA binding / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Simian virus 40 | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Sun, Y. / Zhang, Y. / Hamilton, K. / Walz, T. / Tong, L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2018 Title: Molecular basis for the recognition of the human AAUAAA polyadenylation signal. Authors: Yadong Sun / Yixiao Zhang / Keith Hamilton / James L Manley / Yongsheng Shi / Thomas Walz / Liang Tong / Abstract: Nearly all eukaryotic messenger RNA precursors must undergo cleavage and polyadenylation at their 3'-end for maturation. A crucial step in this process is the recognition of the AAUAAA ...Nearly all eukaryotic messenger RNA precursors must undergo cleavage and polyadenylation at their 3'-end for maturation. A crucial step in this process is the recognition of the AAUAAA polyadenylation signal (PAS), and the molecular mechanism of this recognition has been a long-standing problem. Here, we report the cryo-electron microscopy structure of a quaternary complex of human CPSF-160, WDR33, CPSF-30, and an AAUAAA RNA at 3.4-Å resolution. Strikingly, the AAUAAA PAS assumes an unusual conformation that allows this short motif to be bound directly by both CPSF-30 and WDR33. The A1 and A2 bases are recognized specifically by zinc finger 2 (ZF2) of CPSF-30 and the A4 and A5 bases by ZF3. Interestingly, the U3 and A6 bases form an intramolecular Hoogsteen base pair and directly contact WDR33. CPSF-160 functions as an essential scaffold and preorganizes CPSF-30 and WDR33 for high-affinity binding to AAUAAA. Our findings provide an elegant molecular explanation for how PAS sequences are recognized for mRNA 3'-end formation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 6dnh.cif.gz | 328.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dnh.ent.gz | 246.4 KB | Display | PDB format |
PDBx/mmJSON format | 6dnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6dnh_validation.pdf.gz | 940.5 KB | Display | wwPDB validaton report |
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Full document | 6dnh_full_validation.pdf.gz | 964.1 KB | Display | |
Data in XML | 6dnh_validation.xml.gz | 49.1 KB | Display | |
Data in CIF | 6dnh_validation.cif.gz | 74.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/6dnh ftp://data.pdbj.org/pub/pdb/validation_reports/dn/6dnh | HTTPS FTP |
-Related structure data
Related structure data | 7112MC 7113C 7114C 6blyC 6bm0C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 161074.234 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF1, CPSF160 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q10570 |
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#2: Protein | Mass: 67546.812 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: WDR33, WDC146 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9C0J8 |
#3: Protein | Mass: 27646.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CPSF4, CPSF30, NAR, NEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: O95639 |
#4: RNA chain | Mass: 5361.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Simian virus 40 |
#5: Chemical |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 7.9 / Details: 25 mM Tris-HCl, pH 7.9, 380 mM NaCl, 5 mM DTT | ||||||||||||||||||||||||||||||
Buffer component | Conc.: 0.38 mM / Name: sodium chloride / Formula: NaCl | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.18 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 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: 225000 X / Calibrated magnification: 46729 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 2800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 70 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2468 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1144122 | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173632 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | PDB-ID: 2RHK Pdb chain-ID: C / Accession code: 2RHK / Pdb chain residue range: 56-116 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||
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