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- PDB-21cc: A solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporph... -

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Entry
Database: PDB / ID: 21cc
TitleA solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporphyrin IX ligand
ComponentsRNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
KeywordsRNA / This is a solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporphyrin IX ligand
Function / homologyPROTOPORPHYRIN IX / RNA / RNA (> 10)
Function and homology information
Biological specieschemical production metagenome (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsIwakiri, R. / Wang, S.Y. / Xu, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: A solution NMR model of L-RNA r(UAGGGUUAGGGU) bounding Protoporphyrin IX ligand
Authors: Iwakiri, R. / Wang, S.Y. / Xu, Y.
History
DepositionDec 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 17, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
B: RNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3813
Polymers7,8192
Non-polymers5631
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: RNA chain RNA (5'-R(*UP*AP*GP*GP*GP*UP*UP*AP*GP*GP*GP*U)-3')


Mass: 3909.352 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) chemical production metagenome (others)
#2: Chemical ChemComp-PP9 / PROTOPORPHYRIN IX


Mass: 562.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34N4O4
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentSample state: isotropic / Type: 2D 1H-1H NOESY

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Sample preparation

DetailsType: solution / Contents: 1 mM L-RNA, 100% D2O / Label: 1H / Solvent system: 100% D2O
SampleConc.: 1 mM / Component: L-RNA / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 70 mM / Label: conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBrungerrefinement
Discovery StudioDassault Systemes BIOVIAstructure calculation
MestreLab (Mnova / MestReNova / MestReC)Mike Bernsteinchemical shift assignment
RefinementMethod: molecular dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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