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- PDB-2u1a: RNA BINDING DOMAIN 2 OF HUMAN U1A PROTEIN, NMR, 20 STRUCTURES -

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Basic information

Entry
Database: PDB / ID: 2u1a
TitleRNA BINDING DOMAIN 2 OF HUMAN U1A PROTEIN, NMR, 20 STRUCTURES
ComponentsU1 SMALL NUCLEAR RIBONUCLEOPROTEIN A
KeywordsNUCLEAR PROTEIN / RNA BINDING DOMAIN
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
U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry
AuthorsLu, J. / Hall, K.B.
CitationJournal: Biochemistry / Year: 1997
Title: Tertiary structure of RBD2 and backbone dynamics of RBD1 and RBD2 of the human U1A protein determined by NMR spectroscopy.
Authors: Lu, J. / Hall, K.B.
History
DepositionMar 26, 1997Processing site: BNL
Revision 1.0Sep 26, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / 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 / _pdbx_nmr_software.name / _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
A: U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A


Theoretical massNumber of molelcules
Total (without water)9,8961
Polymers9,8961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40LEAST ERROR FUNCTION
Representative

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Components

#1: Protein U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1 SNRNP A PROTEIN


Mass: 9896.317 Da / Num. of mol.: 1 / Fragment: RNA BINDING DOMAIN 2, RBD2 / Mutation: P2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHA / Plasmid: 1603 TAC2 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM
Production host: Escherichia coli str. K-12 substr. MG1655 (bacteria)
Strain (production host): MG1655 / References: UniProt: P09012

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N EDITED NOESYHMQC
12113C EDITED NOESYHSQC

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Sample preparation

Sample conditionspH: 5.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Varian UNITY500 / Manufacturer: Varian / Model: UNITY500 / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
TinkerPONDERrefinement
Tinkerstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: DISTANCE GEOMETRY WAS PERFORMED USING 5%-PAIRWISE METRIZATION AND A GAUSSIAN TRIAL DISTRIBUTION FOR THE SELECTION OF DISTANCES USING THE PROGRAM DISTGEOM, A COMPONENT OF THE TINKER MOLECULAR ...Details: DISTANCE GEOMETRY WAS PERFORMED USING 5%-PAIRWISE METRIZATION AND A GAUSSIAN TRIAL DISTRIBUTION FOR THE SELECTION OF DISTANCES USING THE PROGRAM DISTGEOM, A COMPONENT OF THE TINKER MOLECULAR MODELING PACKAGE. EMBEDDED STRUCTURES WERE REFINED VERSUS A PENALTY FUNCTION BASED SOLELY ON THE EXPERIMENTAL RESTRAINTS AND LOCAL COVALENT GEOMETRY (BOND LENGTHS, ANGLES, CHIRALITY) OBTAINED FROM A EXTENDED MODEL GENERATED BY QUANTA; NO ENERGY-BASED TERMS WERE INCLUDED. DETAILS OF THE CALCULATIONS AND STRUCTURAL STATISTICS ARE GIVEN IN THE JRNL RECORDS ABOVE.
NMR ensembleConformer selection criteria: LEAST ERROR FUNCTION / Conformers calculated total number: 40 / Conformers submitted total number: 20

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