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Yorodumi- PDB-7xur: The cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xur | ||||||||||||
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Title | The cryo-EM structure of human mini-SNAPc in complex with hU6-1 PSE | ||||||||||||
Components |
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Keywords | TRANSCRIPTION/DNA / snRNA / Transcription factor / Complex / PSE. / TRANSCRIPTION / TRANSCRIPTION-DNA complex | ||||||||||||
Function / homology | Function and homology information snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II general transcription initiation factor activity ...snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / RNA polymerase II general transcription initiation factor activity / transcription by RNA polymerase III / RNA polymerase II transcribes snRNA genes / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / nucleolus / DNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å | ||||||||||||
Authors | Wang, W. / Sun, J.F. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Authors: Jianfeng Sun / Xue Li / Xuben Hou / Sujian Cao / Wenjin Cao / Ye Zhang / Jinyang Song / Manfu Wang / Hao Wang / Xiaodong Yan / Zengpeng Li / Robert G Roeder / Wei Wang / Abstract: In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA ...In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a "wrap-around" mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xur.cif.gz | 196.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xur.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 7xur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xur_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7xur_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7xur_validation.xml.gz | 36.5 KB | Display | |
Data in CIF | 7xur_validation.cif.gz | 52.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xu/7xur ftp://data.pdbj.org/pub/pdb/validation_reports/xu/7xur | HTTPS FTP |
-Related structure data
Related structure data | 33477MC 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
-SnRNA-activating protein complex subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 60780.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC4, SNAP190 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5SXM2 |
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#2: Protein | Mass: 46812.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC3, SNAP50 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q92966 |
#3: Protein | Mass: 33559.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC1, SNAP43 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16533 |
-DNA chain , 2 types, 2 molecules XY
#4: DNA chain | Mass: 10726.930 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#5: DNA chain | Mass: 10803.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 1 types, 2 molecules
#6: Chemical |
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-Details
Has ligand of interest | Y |
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-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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Source (natural) | Organism: Homo sapiens (human) | ||||||||||||||||||||||||
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
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: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 67058 / Symmetry type: POINT | ||||||||||||||||||||||||
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