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- PDB-2xc7: Solution Structure of PHAX-RBD in complex with ssRNA -

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Basic information

Entry
Database: PDB / ID: 2xc7
TitleSolution Structure of PHAX-RBD in complex with ssRNA
Components
  • 5'-(AP*UP*CP*GP)-3'
  • PHOSPHORYLATED ADAPTER RNA EXPORT PROTEIN
KeywordsRNA BINDING PROTEIN / PROTEIN-RNA COMPLEX / NUCLEAR EXPORT
Function / homology
Function and homology information


mRNA cap binding complex binding / snRNA export from nucleus / RNA stabilization / RNA polymerase II transcribes snRNA genes / toxic substance binding / Cajal body / protein transport / snRNP Assembly / ribonucleoprotein complex / neuronal cell body ...mRNA cap binding complex binding / snRNA export from nucleus / RNA stabilization / RNA polymerase II transcribes snRNA genes / toxic substance binding / Cajal body / protein transport / snRNP Assembly / ribonucleoprotein complex / neuronal cell body / RNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
PHAX RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / Phosphorylated adapter RNA export protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / ARIA1.2
AuthorsMourao, A. / Mackereth, C.D. / Varrot, A. / Cusack, S. / Sattler, M.
CitationJournal: RNA / Year: 2010
Title: Structure and RNA Recognition by the Snrna and Snorna Transport Factor Phax.
Authors: Mourao, A. / Varrot, A. / Mackereth, C.D. / Cusack, S. / Sattler, M.
History
DepositionApr 18, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORYLATED ADAPTER RNA EXPORT PROTEIN
P: 5'-(AP*UP*CP*GP)-3'


Theoretical massNumber of molelcules
Total (without water)13,0682
Polymers13,0682
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area79800 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LEAST ENERGY
RepresentativeModel #1

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Components

#1: Protein PHOSPHORYLATED ADAPTER RNA EXPORT PROTEIN / RNA U SMALL NUCLEAR RNA EXPORT ADAPTER PROTEIN


Mass: 11827.519 Da / Num. of mol.: 1 / Fragment: RNA_GG_BIND, RESIDUES 223-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9H814
#2: RNA chain 5'-(AP*UP*CP*GP)-3'


Mass: 1240.802 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCA
121HN(CA)CB
131CBCA(CO)NH
141H(CCCO)NH-TOCSY
151(H)CC(CO)NH- TOCSY
1612D
NMR detailsText: NONE

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Sample preparation

DetailsContents: 90% WATER/10% D2O
Sample conditionsIonic strength: 50 mM / pH: 6.5 / Temperature: 297.0 K

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NMR measurement

NMR spectrometerType: Bruker AMX / Manufacturer: Bruker / Model: AMX / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, READ,RICE,SIMONSON,WARRENrefinement
NMRViewstructure solution
RefinementMethod: ARIA1.2 / Software ordinal: 1 / Details: WATER REFINEMENT
NMR ensembleConformer selection criteria: LEAST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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