2A3J Rna Binding Protein date Jun 24, 2005
title Structure Of Urndesign, A Complete Computational Redesign Of Human U1a Protein
authors G.Varani, N.Dobson, G.Dantas, D.Baker
compound source
Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A
Fragment: Rna Binding Domain, Residues 2-97
Synonym: U1 Snrnp Protein A, U1a Protein, U1-A
Engineered: Yes
Other_details: Computationally Redesigned Variant
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet 29(B)
methodSolution NMR
Gene
Ontology
ChainFunctionProcessComponent
A
  • nucleotide binding
  • nucleic acid binding
  • RNA binding
  • protein binding
  • snRNA binding
  • mRNA splicing, via spliceoso...
  • mRNA processing
  • RNA splicing
  • gene expression
  • nucleus
  • nucleoplasm
  • spliceosomal complex
  • ribonucleoprotein complex
    • Primary referenceHigh-resolution structural validation of the computational redesign of human U1A protein., Dobson N, Dantas G, Baker D, Varani G, Structure. 2006 May;14(5):847-56. PMID:16698546
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (569 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 2A3J
  • Original NMR restraints for 2A3J from PDB
  • Retrieve 2A3J in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2A3J from S2C, [Save to disk]
    • View 2A3J in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 2A3J
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2A3J, from MSDmotif at EBI
  • Fold representative 2a3j from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2a3j_A]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 2A3J: [RRM ] by SMART
  • Alignments of the sequence of 2A3J with the sequences similar proteins can be viewed for 2A3J's classification [SNRPA_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [SNRPA_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 2A3J
  • Community annotation for 2A3J at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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