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- PDB-2y95: Solution structure of AUCG tetraloop hairpin found in human Xist ... -

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Basic information

Entry
Database: PDB / ID: 2y95
TitleSolution structure of AUCG tetraloop hairpin found in human Xist RNA A-repeats essential for X-inactivation
Components5'-R(*GP*GP*CP*GP*CP*AP*UP*CP*GP*GP*CP*GP*CP*C)-3'
KeywordsRNA / X CHROMOSOME INACTIVATION / RNA STEMLOOP
Function / homology: / RNA / RNA (> 10)
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA
AuthorsDuszczyk, 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
DepositionFeb 11, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Other
Revision 1.2Jan 24, 2018Group: Data collection / Experimental preparation
Category: pdbx_nmr_exptl_sample_conditions / pdbx_nmr_spectrometer
Item: _pdbx_nmr_exptl_sample_conditions.ionic_strength / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units ..._pdbx_nmr_exptl_sample_conditions.ionic_strength / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.pH / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_exptl_sample_conditions.pressure / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_spectrometer.manufacturer / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.4Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5'-R(*GP*GP*CP*GP*CP*AP*UP*CP*GP*GP*CP*GP*CP*C)-3'


Theoretical massNumber of molelcules
Total (without water)4,4931
Polymers4,4931
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LEAST RESTRAINT VIOLATION, LOW ENERGY, AGREEMENT WITH CHEMICAL SHIFTS CALCULATED BY NUCHEMICS
Representative

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Components

#1: RNA chain 5'-R(*GP*GP*CP*GP*CP*AP*UP*CP*GP*GP*CP*GP*CP*C)-3' / XIST RNA A-REPEAT / HOMO SAPIENS X (INACTIVE)-SPECIFIC TRANSCRIPT / XIST


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 detailsENGINEERED RESIDUE IN CHAIN A, C 612 TO G ENGINEERED RESIDUE IN CHAIN A, G 619 TO C ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, C 612 TO G ENGINEERED RESIDUE IN CHAIN A, G 619 TO C ENGINEERED RESIDUE IN CHAIN A, U 622 TO C

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY WITH WATERGATE AND WATERFLIPBACK
2212D 1H-13C HSQC
2312D 1H-1H NOESY
3412D 1H-13C HC-TROSY
3512D 1H-1H TOCSY
4612D 1H-15N HSQC
471HNN-COSY
581HNN-COSY
6912D 1H-13C SELECTIVE HSQC
61013D (H)CCH-E.COSY
61113D (H)CCH-TOCSY
61213D HCN
61313D FORWARD DIRECTED (H)CCH-E.COSY
6141HNN- COSY LONG-RANGE
6151HNN-COSY WITH ADIABATIC REFOCUSING
6161TROSY RELAYED (H)CCH-COSY
71712D 1H-13C HMQC
71813D 1H-13C NOESY-HMQC
71913D HCP
72013D HCP SPIN-ECHO-DIFF
82113D (H)CCH-COSY
92212D 1H-13C HC-TROSY
NMR detailsText: 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

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Sample preparation

Details
Solution-IDContents
190% H2O/10% D2O
2100% D2O
390% H2O/10% D2O
490% H2O/10% D2O
5100% D2O
6100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1100 mM61.0 atm278.0 K
2100 mM61.0 atm298.0 K
3100 mM61.0 atm298.0 K
4100 mM61.0 atm278.0 K
5100 mM61.0 atm278.0 K
6100 mM61.0 atm298.0 K
7100 mM61.0 atm298.0 K
8100 mM61.0 atm298.0 K
9100 mM61.0 atm298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DRXBrukerDRX9002
Bruker DRXBrukerDRX6003
Bruker DRXBrukerDRX6004
Bruker DRXBrukerDRX6005
Bruker DRXBrukerDRX6006
Bruker DRXBrukerDRX9007
Bruker DMXBrukerDMX8008
Bruker DRXBrukerDRX6009

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Processing

NMR software
NameVersionDeveloperClassification
AmberD.A.CASE,T.A.DARDEN,T.E.CHEATHAM,III, C.L.SIMMERLING,J.WANG,R.E.DUKE,R.LUO, R.C.WALKER,W.ZHANG,K.M.MERZ,B.P.ROBERTS, B.WANG,S.HAYIK,A.ROITBERG,G.SEABRA, I.KOLOSSVARY,K.F.WONG,F.PAESANI,J.VANICEK, X.WU,S.R.BROZELL,T.STEINBRECHER,H.GOHLKE, Q.CAI,X.YE,J.WANG,M.-J.HSIEH,G.CUI,D.R.ROE, D.H.MATHEWS,M.G.SEETIN,C.SAGUI,V.BABIN, A. LUCHKO,S.GUSAROV,A.KOVALENKO,P.A.KOLLMAN.refinement
NMRPipestructure solution
NMRViewstructure solution
ARIA1.2structure solution
Amberstructure solution
RefinementMethod: ARIA / Software ordinal: 1
Details: 20 ARIA-CALCULATED STRUCTURES WERE CHOSEN BASED UPON LOW RESTRAINT VIOLATION AND LOW ENERGY FOR REFINEMENT WITH AMBER
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION, LOW ENERGY, AGREEMENT WITH CHEMICAL SHIFTS CALCULATED BY NUCHEMICS
Conformers calculated total number: 100 / Conformers submitted total number: 10

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