+Open data
-Basic information
Entry | Database: PDB / ID: 1aud | |||||||||
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Title | U1A-UTRRNA, NMR, 31 STRUCTURES | |||||||||
Components |
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Keywords | RNA 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR | |||||||||
Authors | Allain, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aud.cif.gz | 899.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aud.ent.gz | 749.6 KB | Display | PDB format |
PDBx/mmJSON format | 1aud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aud_validation.pdf.gz | 386 KB | Display | wwPDB validaton report |
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Full document | 1aud_full_validation.pdf.gz | 813.1 KB | Display | |
Data in XML | 1aud_validation.xml.gz | 97.4 KB | Display | |
Data in CIF | 1aud_validation.cif.gz | 130.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/1aud ftp://data.pdbj.org/pub/pdb/validation_reports/au/1aud | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: RNA chain | Mass: 9596.738 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR |
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-Sample preparation
Sample conditions | Ionic strength: 50 mM NACL / Temperature units: K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
Software |
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NMR software |
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Refinement | Software 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 ensemble | Conformer selection criteria: LOWEST TOTAL ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 31 |