3PLA Transferase Rna date Nov 15, 2010
title Crystal Structure Of A Catalytically Active Substrate-Bound Rnp From Sulfolobus Solfataricus
authors J.Lin, S.Lai, R.Jia, A.Xu, L.Zhang, J.Lu, K.Ye
compound source
Molecule: Pre Mrna Splicing Protein
Chain: A, B, K
Fragment: Unp Residues 1-380
Synonym: Nop5
Engineered: Yes
Mutation: Yes
Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Sso0939
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: 50s Ribosomal Protein L7ae
Chain: C, D, L
Engineered: Yes
Mutation: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 555311
Strain: 982
Gene: Rpl7ae, Ssol_1068
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Fibrillarin-Like Rrnatrna 2'-O-Methyltransferase
Chain: E, F, M
Synonym: Fib
Ec: 2.1.1.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Sulfolobus Solfataricus
Organism_taxid: 2287
Gene: Flpa, Sso0940, C33_014
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Ril+
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Cd Guide Rna
Chain: G, H, N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: In Vitro Transcription

Molecule: Rna (5'-R(Cpcpapupgpapgpupgpu)-3')
Chain: I, J, O
Engineered: Yes
Other_details: Substrate Rna

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Chemical Synthesis
symmetry Space Group: P 41 21 2
R_factor 0.248 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
241.199 241.199 145.408 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.15 Å
ligand SAH enzyme Transferase E.C.2.1.1 BRENDA
Gene C33 ; SSOL
Gene
Ontology
ChainFunctionProcessComponent
A, K, B


C, D, L
  • ribonuclease P activity


  • F, E, M


    Primary referenceStructural basis for site-specific ribose methylation by box C/D RNA protein complexes., Lin J, Lai S, Jia R, Xu A, Zhang L, Lu J, Ye K, Nature. 2011 Jan 27;469(7331):559-563. PMID:21270896
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (843 Kb) [Save to disk]
  • Biological Unit Coordinates (3pla.pdb1.gz) 554 Kb
  • Biological Unit Coordinates (3pla.pdb2.gz) 556 Kb
  • LPC: Ligand-Protein Contacts for 3PLA
  • CSU: Contacts of Structural Units for 3PLA
  • Structure Factors (1144 Kb)
  • Retrieve 3PLA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3PLA from S2C, [Save to disk]
  • Re-refined 3pla structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3PLA 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 3PLA
  • 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 3PLA, from MSDmotif at EBI
  • Fold representative 3pla from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3pla_L] [3pla_O] [3pla_M] [3pla_A] [3pla_C] [3pla_F] [3pla_B] [3pla_I] [3pla_N] [3pla_G] [3pla] [3pla_H] [3pla_K] [3pla_E] [3pla_J] [3pla_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3PLA: [Fibrillarin] [NOSIC ] by SMART
  • Other resources with information on 3PLA
  • Community annotation for 3PLA 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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