[English] 日本語
Yorodumi- PDB-2y95: Solution structure of AUCG tetraloop hairpin found in human Xist ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2y95 | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Solution structure of AUCG tetraloop hairpin found in human Xist RNA A-repeats essential for X-inactivation | ||||||||||||||||||||
Components | 5'-R(*Keywords | RNA / X CHROMOSOME INACTIVATION / RNA STEMLOOP | Function / homology | : / RNA / RNA (> 10) | Function and homology information Biological species | HOMO SAPIENS (human) | Method | SOLUTION NMR / ARIA | Authors | Duszczyk, M.M. / Sattler, M. | Citation | Journal: RNA / Year: 2011 Title: The Xist RNA A-Repeat Comprises a Novel Aucg Tetraloop Fold and a Platform for Multimerization. Authors: Duszczyk, M.M. / Wutz, A. / Rybin, V. / Sattler, M. #1: Journal: Biomol.NMR Assign. / Year: 2012 Title: (1)H, (13)C, (15)N and (31)P Chemical Shift Assignments of a Human Xist RNA A-Repeat Tetraloop Hairpin Essential for X-Chromosome Inactivation. Authors: Duszczyk, M.M. / Sattler, M. History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2y95.cif.gz | 91 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2y95.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 2y95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y9/2y95 ftp://data.pdbj.org/pub/pdb/validation_reports/y9/2y95 | HTTPS FTP |
---|
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: RNA chain | Mass: 4492.739 Da / Num. of mol.: 1 / Fragment: HAIRPIN 1, RESIDUES 609-622 / Mutation: YES / Source method: obtained synthetically Details: HAIRPIN 1 FROM THE 6TH HUMAN A-REPEAT CORRESPONDING TO NUCLEOTIDES 609-622 IN M97168.1 GENBANK ENTRY. THE THIRD G-C BASE-PAIR IS REPLACED BY C-G TO FACILITATE CHEMICAL SHIFT ASSIGNMENTS AND ...Details: HAIRPIN 1 FROM THE 6TH HUMAN A-REPEAT CORRESPONDING TO NUCLEOTIDES 609-622 IN M97168.1 GENBANK ENTRY. THE THIRD G-C BASE-PAIR IS REPLACED BY C-G TO FACILITATE CHEMICAL SHIFT ASSIGNMENTS AND THE CLOSING G-U BASE PAIR IS REPLACED BY G-C Source: (synth.) HOMO SAPIENS (human) / References: GenBank: 340393 |
---|---|
Compound details | ENGINEERED RESIDUE IN CHAIN A, C 612 TO G ENGINEERED RESIDUE IN CHAIN A, G 619 TO C ENGINEERED ...ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR details | Text: 100 INITIAL STRUCTURES WERE CALCULATED USING ARIA, 20 WERE SELECTED FOR REFINEMENT WITH AMBER, OF WHICH 10 WERE SELECTED FOR DEPOSITION BASED ON LOW ENERGY CRITERIA AND AGREEMENT BETWEEN ...Text: 100 INITIAL STRUCTURES WERE CALCULATED USING ARIA, 20 WERE SELECTED FOR REFINEMENT WITH AMBER, OF WHICH 10 WERE SELECTED FOR DEPOSITION BASED ON LOW ENERGY CRITERIA AND AGREEMENT BETWEEN CALCULATED AND EXPERIMENTAL CHEMICAL SHIFTS |
-Sample preparation
Details |
| ||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample conditions |
|
-NMR measurement
NMR spectrometer |
|
---|
-Processing
NMR software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: ARIA / Software ordinal: 1 Details: 20 ARIA-CALCULATED STRUCTURES WERE CHOSEN BASED UPON LOW RESTRAINT VIOLATION AND LOW ENERGY FOR REFINEMENT WITH AMBER | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: LEAST RESTRAINT VIOLATION, LOW ENERGY, AGREEMENT WITH CHEMICAL SHIFTS CALCULATED BY NUCHEMICS Conformers calculated total number: 100 / Conformers submitted total number: 10 |