1U6B Structural Protein Rna date Jul 29, 2004
title Crystal Structure Of A Self-Splicing Group I Intron With Bot
authors P.L.Adams, M.R.Stahley, A.B.Kosek, J.Wang, S.A.Strobel
compound source
Molecule: 197-Mer
Chain: B
Fragment: Group I Intron
Engineered: Yes
Synthetic: Yes
Other_details: Rna Was Is Transcribed By T7 Rna Polymerase.

Molecule: 5'-R(Apapgpcpcpapcpapcpapapapcpcpa Gp Gpcpc)-3';
Chain: C
Fragment: Group I Exon
Engineered: Yes

Synthetic: Yes

Molecule: 5'-R(Cpap(5mu))-3'
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: U1 Small Nuclear Ribonucleoprotein A
Chain: A
Synonym: U1 Snrnp Protein A, U1a Protein, U1-A
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpa
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11
symmetry Space Group: P 41 2 2
R_factor 0.246 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.541 108.541 249.158 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.10 Å
ligand 5MU, A23, GTP, K, MG enzyme
note 1U6B (Molecule of the Month:pdb65)supersedes 1T42
Primary referenceCrystal structure of a self-splicing group I intron with both exons., Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA, Nature 2004 Jul 1;430(6995):45-50. Epub 2004 Jun 2. PMID:15175762
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (122 Kb) [Save to disk]
  • Biological Unit Coordinates (1u6b.pdb1.gz) 114 Kb
  • LPC: Ligand-Protein Contacts for 1U6B
  • CSU: Contacts of Structural Units for 1U6B
  • Likely Quarternary Molecular Structure file(s) for 1U6B
  • Structure Factors (199 Kb)
  • Retrieve 1U6B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U6B from S2C, [Save to disk]
  • Re-refined 1u6b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1U6B 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.
  • Visual 3D analysis of 1U6B
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1U6B, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u6ba_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1u6b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1u6b_D] [1u6b_A] [1u6b_B] [1u6b] [1u6b_C]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1U6B: [RRM ] by SMART
  • Alignments of the sequence of 1U6B with the sequences similar proteins can be viewed for 1U6B'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 1U6B
  • Community annotation for 1U6B 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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