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- PDB-1pqn: dominant negative human hDim1 (hDim1 1-128) -

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Basic information

Entry
Database: PDB / ID: 1pqn
Titledominant negative human hDim1 (hDim1 1-128)
ComponentsSpliceosomal U5 snRNP-specific 15 kDa protein
KeywordsCELL CYCLE / dim1 / dominant negative / pre-mRNA splicing / snRNP / U5-15k SPLICEOSOMAL PROTEIN / THIOREDOXIN / TRANSCRIPTION / cleavage
Function / homology
Function and homology information


RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cell cycle ...RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / cell cycle / cell division / nucleoplasm / nucleus / cytosol
Similarity search - Function
Dim1 family / Mitosis protein DIM1 / Mitosis protein DIM1 / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-like protein 4A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsZhang, Y.Z. / Cheng, H. / Gould, K.L. / Golemis, E.A. / Roder, H.
Citation
Journal: Biochemistry / Year: 2003
Title: Structure, stability and function of hDim1 investigated by NMR, circular dichroism and mutational analysis
Authors: Zhang, Y.Z. / Cheng, H. / Gould, K.L. / Golemis, E.A. / Roder, H.
#1: Journal: Physiol.Genomics / Year: 1999
Title: The evolutionarily conserved Dim1 protein defines a novel branch of the thioredoxin fold superfamily
Authors: ZHANG, Y.Z. / GOULD, K.L. / DUNBRACK JR., R.L. / CHENG, H. / RODER, H. / GOLEMIS, E.A.
History
DepositionJun 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spliceosomal U5 snRNP-specific 15 kDa protein


Theoretical massNumber of molelcules
Total (without water)14,9721
Polymers14,9721
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)20 / 120structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Spliceosomal U5 snRNP-specific 15 kDa protein / DIM1 protein homolog / Thioredoxin-like U5 snRNP protein U5-15kD


Mass: 14972.187 Da / Num. of mol.: 1 / Fragment: dominant negative human hDim1 / Mutation: deltaC14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DIM1 / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P83876

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
131HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM hDim1 1-128,U-15N; 10mM phosphate buffer; 95% H2O, 5% D2O, 0.2% 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.04% NaN395% H2O/5% D2O
21mM hDim1 1-128,U-15N,13C; 10mM phosphate buffer; 95% H2O, 5% D2O, 0.2% 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.04% NaN395% H2O/5% D2O
31mM hDim1 1-128,U-13C; 10mM phosphate buffer; 100% D2O, 0.2% 2,2-dimethyl-2-silapentane-5-sulfonate (DSS), 0.04% NaN3100% D2O
Sample conditionspH: 7.65 / Pressure: ambient / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2Brukercollection
Felix98Accelrysprocessing
CNS1Brungerstructure solution
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1445 restraints, 1294 are NOE-derived distance constraints, 67 dihedral angle restraints,84 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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