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Yorodumi- PDB-6xh1: Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xh1 | ||||||
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Title | Co-crystal structure of HIV-1 TAR RNA in complex with lab-evolved RRM TBP6.7 mutant | ||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / PROTEIN-RNA COMPLEX / TAR RNA / LAB-EVOLVED PROTEIN / ARGININE FORK / BETA HAIRPIN / MAJOR-GROOVE READOUT / BASE TRIPLE / U1A / HIV-1 / TRANS- ACTIVATION / RNA RECOGNITION MOTIF / RRM / RNA BINDING PROTEIN-RNA COMPLEX / RNA BINDING PROTEIN | ||||||
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 | Homo sapiens (human) Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.601 Å | ||||||
Authors | Chavali, S.S. / Jenkins, J.L. / Wedekind, J.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: Co-crystal structures of HIV TAR RNA bound to lab-evolved proteins show key roles for arginine relevant to the design of cyclic peptide TAR inhibitors. Authors: Chavali, S.S. / Mali, S.M. / Jenkins, J.L. / Fasan, R. / Wedekind, J.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xh1.cif.gz | 70.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xh1.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 6xh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xh/6xh1 ftp://data.pdbj.org/pub/pdb/validation_reports/xh/6xh1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10042.720 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09012*PLUS |
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#2: RNA chain | Mass: 8657.167 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: 0.2 M Ammonium Nitrate, 20% (w/v) PEG-3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2019 Details: Rh coated collimating mirrors, K-B focusing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.85 Å / Num. obs: 7660 / % possible obs: 96.5 % / Redundancy: 7.9 % / CC1/2: 0.986 / Rpim(I) all: 0.065 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 944 / CC1/2: 0.403 / Rpim(I) all: 0.55 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.601→39.85 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 24.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 146.83 Å2 / Biso mean: 48.9115 Å2 / Biso min: 22.19 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.601→39.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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