3NMU Transferase Rna date Jun 22, 2010
title Crystal Structure Of Substrate-Bound Halfmer Box Cd Rnp
authors H.Li, S.Xue, R.Wang
compound source
Molecule: Nop5nop56 Related Protein
Chain: A, B
Engineered: Yes
Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Pf0060
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: 50s Ribosomal Protein L7ae
Chain: C, G
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Rpl7ae, Pf1367
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (34-Mer)
Chain: D, E
Engineered: Yes
Other_details: Box Cd Rna

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261

Molecule: Fibrillarin-Like Rrnatrna 2'-O-Methyltransferase
Chain: F, J
Ec: 2.1.1.-
Engineered: Yes

Organism_scientific: Pyrococcus Furiosus
Organism_taxid: 2261
Gene: Flpa, Pf0059
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'-R(Gpapgpcpupupcpapapcpgpgpc)
Chain: I, K
Engineered: Yes

Synthetic: Yes
Organism_taxid: 32630
Other_details: The Rna Was Chemically Synthesized
symmetry Space Group: C 1 2 1
R_factor 0.222 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
293.506 94.054 96.810 90.00 101.47 90.00
method X-Ray Diffractionresolution 2.73 Å
ligand SAM enzyme Transferase E.C.2.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C, G
  • ribonuclease P activity


  • F, J


    Primary referenceStructural basis for substrate placement by an archaeal box C/D ribonucleoprotein particle., Xue S, Wang R, Yang F, Terns RM, Terns MP, Zhang X, Maxwell ES, Li H, Mol Cell. 2010 Sep 24;39(6):939-49. PMID:20864039
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (280 Kb) [Save to disk]
  • Biological Unit Coordinates (3nmu.pdb1.gz) 139 Kb
  • Biological Unit Coordinates (3nmu.pdb2.gz) 138 Kb
  • Biological Unit Coordinates (3nmu.pdb3.gz) 273 Kb
  • LPC: Ligand-Protein Contacts for 3NMU
  • CSU: Contacts of Structural Units for 3NMU
  • Structure Factors (594 Kb)
  • Retrieve 3NMU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NMU from S2C, [Save to disk]
  • Re-refined 3nmu structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NMU 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 3NMU
  • 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 3NMU, from MSDmotif at EBI
  • Fold representative 3nmu from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nmu_D] [3nmu_I] [3nmu_J] [3nmu_K] [3nmu_F] [3nmu_B] [3nmu_A] [3nmu_E] [3nmu_G] [3nmu] [3nmu_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NMU: [Fibrillarin] [NOSIC ] by SMART
  • Other resources with information on 3NMU
  • Community annotation for 3NMU 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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