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- PDB-2a3j: Structure of URNdesign, a complete computational redesign of huma... -

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Basic information

Entry
Database: PDB / ID: 2a3j
TitleStructure of URNdesign, a complete computational redesign of human U1A protein
ComponentsU1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / COMPUTATIONALLY DESIGNED PROTEIN / RRM / U1A
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 / simulated annealing
AuthorsVarani, G. / Dobson, N. / Dantas, G. / Baker, D.
CitationJournal: Structure / Year: 2006
Title: High-Resolution Structural Validation of the Computational Redesign of Human U1A Protein
Authors: Dobson, N. / Dantas, G. / Baker, D. / Varani, G.
History
DepositionJun 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model
Remark 999 SEQUENCE According to authors, the protein was designed using (Rosetta), retaining the same ... SEQUENCE According to authors, the protein was designed using (Rosetta), retaining the same structure as human U1A but a different sequence (34% sequence homology). The structure corresponds to residues 2-97 in the native protein followed by a HIS TAG.

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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)13,9481
Polymers13,9481
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein U1 small nuclear ribonucleoprotein A / U1 snRNP protein A / U1A protein / U1-A


Mass: 13948.337 Da / Num. of mol.: 1 / Fragment: RNA binding domain, residues 2-97
Source method: isolated from a genetically manipulated source
Details: Computationally redesigned variant / Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET 29(b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09012

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
12115N-HSQC
13213C-15N-HSQC
142HNCA(CO)CB
152HNCA
162HNCO
172HBHA(CO)NH
182CBCA(CO)NH
1923D (H)CCH-TOCSY
11023D 13C-edited NOESY
11113D 15N-EDITED NOESY
11212D NOESY IN D2O

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Sample preparation

Details
Solution-IDContentsSolvent system
1U-15N,variant of U1A, 50 mM Sodium Phosphate,5% D2O5% D2O in water
2U-15N, 13C, variant of U1A, 50 mM Sodium Phosphate, 5% D2O5% D2O in water
Sample conditionsIonic strength: 50 mM sodium phosphate / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE7502
Varian AMXVarianAMX6003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1DELAGLIOdata analysis
CYANA1.1, 2.0GUNTERTrefinement
CANDID1.1, 2.0structure solution
CYANA1.1, 2.0structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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