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- PDB-1aud: U1A-UTRRNA, NMR, 31 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 1aud
TitleU1A-UTRRNA, NMR, 31 STRUCTURES
Components
  • RNA 3UTR
  • U1A 102
KeywordsRNA BINDING PROTEIN/RNA / COMPLEX (RIBONUCLEOPROTEIN-RNA) / RNP DOMAIN / RNA BINDING PROTEIN-RNA COMPLEX
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
AuthorsAllain, F.H.-T. / Gubser, C.C. / Howe, P.W.A. / Nagai, K. / Neuhaus, D. / Varani, G.
Citation
Journal: EMBO J. / Year: 1997
Title: Structural basis of the RNA-binding specificity of human U1A protein.
Authors: Allain, F.H. / Howe, P.W. / Neuhaus, D. / Varani, G.
#1: Journal: J.BIOMOL.NMR / Year: 1998
Title: Determination of the NMR Structure of the Complex between U1A Protein and its RNA Polyadenylation Inhibition Element
Authors: Howe, P.W.A. / Allain, F.H.T. / Varani, G. / Neuhaus, D.
#2: Journal: Nature / Year: 1996
Title: Specificity of Ribonucleoprotein Interaction Determined by RNA Folding During Complex Formulation
Authors: Allain, F.H. / Gubser, C.C. / Howe, P.W. / Nagai, K. / Neuhaus, D. / Varani, G.
#3: Journal: Nature / Year: 1994
Title: Crystal Structure at 1.92 A Resolution of the RNA-Binding Domain of the U1A Spliceosomal Protein Complexed with an RNA Hairpin
Authors: Oubridge, C. / Ito, N. / Evans, P.R. / Teo, C.H. / Nagai, K.
History
DepositionAug 22, 1997Processing site: BNL
SupersessionFeb 25, 1998ID: 1NUM
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: RNA 3UTR
A: U1A 102


Theoretical massNumber of molelcules
Total (without water)21,2102
Polymers21,2102
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)31 / 50LOWEST TOTAL ENERGY
Representative

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Components

#1: RNA chain RNA 3UTR / UUCG TETRALOOP / ONLY BOX 1 OF 3'UTR RNA


Mass: 9596.738 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein U1A 102 / U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A


Mass: 11613.582 Da / Num. of mol.: 1 / Fragment: RESIDUES 1 - 102 OF U1A / Mutation: Y30H, Q35R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: BL21 (DE3) / Cell line: BL21 / Gene: U1A 1-102 / Plasmid: PET13A / Gene (production host): T7 / Production host: Escherichia coli (E. coli) / References: UniProt: P09012

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 50 mM NACL / Temperature units: K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX500BrukerAMX5005001
Bruker DMX600BrukerDMX6006002

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
XPLOR3.1structure solution
RefinementSoftware ordinal: 1
Details: STARTING WITH 50 STRUCTURES WITH RANDOMISED BACKBONE TORSION ANGLES ON BOTH THE RNA AND THE PROTEIN COMPONENTS, 31 STRUCTURES WERE FOUND TO HAVE CONVERGED. THE X-PLOR PROTOCOL START WITH A ...Details: STARTING WITH 50 STRUCTURES WITH RANDOMISED BACKBONE TORSION ANGLES ON BOTH THE RNA AND THE PROTEIN COMPONENTS, 31 STRUCTURES WERE FOUND TO HAVE CONVERGED. THE X-PLOR PROTOCOL START WITH A PERIOD OF SIMULATED ANNEALING WITH ONLY DISTANCE CONSTRAINTS (249 1 INCLUDING 123 INTERMOLECULAR) FOLLOWED BY A PERIOD OF REFINEMENT WHERE 110 DIHEDRAL CONSTRAINTS DERIVED FROM J COUPLING ANALYSIS AND PHOSPHORUS CHEMICAL SHIFT VALUE WERE ADDED (IN THE RNA ONLY). NO DIHEDRAL ANGLE VIOLATIONS AND AN AVERAGE OF 4 NOE VIOLA TIONS BETWEEN 0.2 - 0.5 A WERE FOUND IN THE 31 CONVERGED STRUCTURES.
NMR ensembleConformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 31

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