1SJ4 Translation Rna date Mar 02, 2004
title Crystal Structure Of A C75u Mutant Hepatitis Delta Virus Rib Precursor, In Cu2+ Solution
authors A.Ke, K.Zhou, F.Ding, J.H.Cate, J.A.Doudna
compound source
Molecule: Precursor Form Of The Hepatitis Delta Virus Riboz
Chain: R
Engineered: Yes
Mutation: Yes
Organism_scientific: Hepatitis Delta Virus
Organism_taxid: 12475
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh5alpha
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Puc19-Pt3
Other_details: C75u In Vitro Transcription

Molecule: Small Nuclear Ribonucleoprotein A
Chain: P
Fragment: Rna Binding Domain
Synonym: U1 Snrnp Protein A; U1a Protein; U1-A; Small Nucle Ribonucleoprotein Polypeptide A;
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Snrpa
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Other_details: Y31h, Q36r
symmetry Space Group: H 3 2
R_factor 0.250 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
108.566 108.566 190.319 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.70 Å
Primary referenceA conformational switch controls hepatitis delta virus ribozyme catalysis., Ke A, Zhou K, Ding F, Cate JH, Doudna JA, Nature 2004 May 13;429(6988):201-5. PMID:15141216
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (1sj4.pdb1.gz) 47 Kb
  • CSU: Contacts of Structural Units for 1SJ4
  • Likely Quarternary Molecular Structure file(s) for 1SJ4
  • Structure Factors (141 Kb)
  • Retrieve 1SJ4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SJ4 from S2C, [Save to disk]
  • Re-refined 1sj4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SJ4 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 1SJ4
  • 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 1SJ4, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sj4p_, region P [Jmol] [rasmolscript] [script source]
  • Fold representative 1sj4 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: [1sj4_R] [1sj4_P] [1sj4]
  • SWISS-PROT database: [P09012]
  • Domain organization of [SNRPA_HUMAN] by SWISSPFAM
  • Domain found in 1SJ4: [RRM ] by SMART
  • Alignments of the sequence of 1SJ4 with the sequences similar proteins can be viewed for 1SJ4'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 1SJ4
  • Community annotation for 1SJ4 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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