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Yorodumi- PDB-7d7v: Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d7v | ||||||
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Title | Crystal Structure of the Domain1 of NAD+ Riboswitch with nicotinamide adenine dinucleotide (NAD+) and U1A protein | ||||||
Components |
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Keywords | RNA / riboswitch / RNA structure / RNA folding / RNA-ligand interactions / RNA crystallography | ||||||
Function / homology | Function and homology information U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Acidobacterium capsulatum ATCC 51196 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Chen, H. / Ren, A.M. | ||||||
Funding support | China, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2020 Title: Structural distinctions between NAD+ riboswitch domains 1 and 2 determine differential folding and ligand binding. Authors: Chen, H. / Egger, M. / Xu, X. / Flemmich, L. / Krasheninina, O. / Sun, A. / Micura, R. / Ren, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d7v.cif.gz | 71.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d7v.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7d7v_validation.pdf.gz | 3.6 MB | Display | wwPDB validaton report |
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Full document | 7d7v_full_validation.pdf.gz | 3.6 MB | Display | |
Data in XML | 7d7v_validation.xml.gz | 9.5 KB | Display | |
Data in CIF | 7d7v_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/7d7v ftp://data.pdbj.org/pub/pdb/validation_reports/d7/7d7v | HTTPS FTP |
-Related structure data
Related structure data | 7d7wC 7d7xC 7d7yC 7d7zC 7d81C 7d82C C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain / Protein , 2 types, 2 molecules AC
#1: RNA chain | Mass: 18270.900 Da / Num. of mol.: 1 / Mutation: G4del A51del G29C30G31A32 TO AUUGCACUCC Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acidobacterium capsulatum ATCC 51196 (bacteria) Production host: in vitro transcription vector pT7-TP(deltai) (others) |
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#2: Protein | Mass: 10681.421 Da / Num. of mol.: 1 / Mutation: Y27H, Q32R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: bacterium (bacteria) / References: UniProt: P09012 |
-Non-polymers , 4 types, 51 molecules
#3: Chemical | ChemComp-GTP / | ||||
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#4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-NAD / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.92 Å3/Da / Density % sol: 68.59 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Mg(OAc)2, 0.1 M C2H6AsNaO2, pH 6.5, 30% MPD |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 28, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 12481 / % possible obs: 99.6 % / Redundancy: 21.4 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.016 / Rrim(I) all: 0.084 / Χ2: 0.842 / Net I/σ(I): 5.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 139.72 Å2 / Biso mean: 76.524 Å2 / Biso min: 31.73 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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LS refinement shell | Resolution: 2.8→3.0795 Å
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