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- PDB-1dz5: The NMR structure of the 38KDa U1A protein-PIE RNA complex reveal... -

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Basic information

Entry
Database: PDB / ID: 1dz5
TitleThe NMR structure of the 38KDa U1A protein-PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein
Components
  • PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*CP*CP* CP*GP*GP*AP*GP*UP*CP*UP*C)-3')
  • U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
KeywordsRIBONUCLEOPROTEIN/RNA / RIBONUCLEOPROTEIN-RNA COMPLEX / POLYADENYLATION / PROTEIN PROTEIN INTERACTION / RNA PROTEIN INTERACTION
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
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits ...U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / RESTRAINED MOLECULAR DYNAMICS
AuthorsVarani, L. / Gunderson, S.I. / Mattaj, I.W. / Kay, L.E. / Neuhaus, D. / Varani, G.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: The NMR Structure of the 38kDa U1A Protein-Pie RNA Complex Reveals the Basis of Cooperativity in Regulation of Polyadenylation by Human U1A Protein
Authors: Varani, L. / Gunderson, S.I. / Mattaj, I.W. / Kay, L.E. / Neuhaus, D. / Varani, G.
History
DepositionFeb 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
B: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
C: PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*CP*CP* CP*GP*GP*AP*GP*UP*CP*UP*C)-3')
D: PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*CP*CP* CP*GP*GP*AP*GP*UP*CP*UP*C)-3')


Theoretical massNumber of molelcules
Total (without water)37,2944
Polymers37,2944
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)13 / 50AGREEMENT WITH EXPERIMENTAL DATA
Representative

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Components

#1: Protein U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1 SNRNP A / U1-A / U1A


Mass: 11613.582 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-102 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET13A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09012
#2: RNA chain PIE, RNA (5'-R(*GP*AP*GP*AP*CP*AP*UP*UP*GP*CP*AP*CP*CP* CP*GP*GP*AP*GP*UP*CP*UP*C)-3')


Mass: 7033.242 Da / Num. of mol.: 2 / Fragment: 3' UTR POLYADENYLATION INHIBITION ELEMENT / Mutation: YES / Source method: obtained synthetically / Details: PRODUCED BY IN VITRO TRANSCRIPTION / Source: (synth.) HOMO SAPIENS (human)
Compound detailsMUTATIONS IN CHAIN A,B: Y31H, Q36R MUTATIONS IN CHAIN C: U18C, A21G MUTATIONS IN CHAIN D: U47C

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D FILTERED NOESY
121HSQCS
131HALF-FILTER EXPERIMENTS
1412D NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 15N, 13C AND 2D LABELED SAMPLES. DIFFERENT LABELLED SPECIES WERE MIXED IN DIFFERENT EXPERIMENTS. TRIPLE RESONANCE EXPERIMENTS COULD NOT BE USED DUE TO THE ...Text: THE STRUCTURE WAS DETERMINED USING 15N, 13C AND 2D LABELED SAMPLES. DIFFERENT LABELLED SPECIES WERE MIXED IN DIFFERENT EXPERIMENTS. TRIPLE RESONANCE EXPERIMENTS COULD NOT BE USED DUE TO THE SIZE OF THE COMPLEX; TROSY WAS NOT AVAILABLE WHEN MOST OF THE ASSIGNMENT WAS COMPLETED.

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Sample preparation

DetailsContents: 10MM PHOSPHATE BUFFER
Sample conditionsIonic strength: 10MM PHOSPHATE BUFFER / pH: 6.0 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8.1BRUNGERrefinement
XPLOR3.8.1structure solution
RefinementMethod: RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1 / Details: DETAILS CAN BE FOUND IN THE JOURNAL CITATION ABOVE
NMR ensembleConformer selection criteria: AGREEMENT WITH EXPERIMENTAL DATA
Conformers calculated total number: 50 / Conformers submitted total number: 13

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