2NN6 Hydrolase Transferase date Oct 23, 2006
title Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
authors C.D.Lima
compound source
Molecule: Polymyositisscleroderma Autoantigen 1
Chain: A
Synonym: Ribosomal Rna-Processing Protein 45, Rrp45, Pmscl
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Pmscl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet-1 (Novagen)

Molecule: Exosome Complex Exonuclease Rrp41
Chain: B
Synonym: Ribosomal Rna-Processing Protein 41, Exosome Compo P12a;
Ec: 3.1.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc4, Rrp41, Ski6
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet-1 (Novagen)

Molecule: Exosome Complex Exonuclease Rrp43
Chain: C
Synonym: Ribosomal Rna-Processing Protein 43, Exosome Compo P9, Opa-Interacting Protein 2, Oip2;
Ec: 3.1.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc8, Oip2, Rrp43
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3 (Smt3 Fusion)

Molecule: Exosome Complex Exonuclease Rrp46
Chain: D
Synonym: Ribosomal Rna-Processing Protein 46, Exosome Compo P12b, Chronic Myelogenous Leukemia Tumor Antigen 28;
Ec: 3.1.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc5, Cml28, Rrp46
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psmt3 (Smt3-Fusion)

Molecule: Exosome Complex Exonuclease Rrp42
Chain: E
Synonym: Ribosomal Rna-Processing Protein 42, Exosome Compo P8;
Ec: 3.1.13.-
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc7, Kiaa0116, Rrp42
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1 (Novagen)

Molecule: Exosome Component 6
Chain: F
Synonym: Mtr3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc6
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Star
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1 (Novagen)

Molecule: Exosome Complex Exonuclease Rrp40
Chain: G
Synonym: Ribosomal Rna-Processing Protein 40, Exosome Compo P10;
Ec: 3.1.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc3, Rrp40
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1 (Novagen)

Molecule: Exosome Complex Exonuclease Rrp4
Chain: H
Synonym: Ribosomal Rna-Processing Protein 4, Exosome Compon
Ec: 3.1.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc2, Rrp4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1 (Novagen)

Molecule: 3'-5' Exoribonuclease Csl4 Homolog
Chain: I
Synonym: Exosome Component 1
Ec: 3.1.13.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Strain: Placental Cdna (Ambion, Inc)
Gene: Exosc1, Csl4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Codonplus-Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Prsfduet-1 (Novagen)
symmetry Space Group: P 4 3 2
R_factor 0.291 R_Free 0.344
crystal
cell
length a length b length c angle alpha angle beta angle gamma
307.800 307.800 307.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.35 Å
ligand
enzyme Hydrolase E.C.3.1.13 BRENDA
note 2NN6 (Molecule of the Month:pdb86)
Gene
Ontology
ChainFunctionProcessComponent
A


B
  • 3'-5'-exoribonuclease activi...
  • exoribonuclease activity


  • C


    D
  • 3'-5'-exoribonuclease activi...
  • exoribonuclease activity


  • E


    F
  • exoribonuclease activity


  • G


    H


    I
  • exoribonuclease activity


  • Primary referenceReconstitution, activities, and structure of the eukaryotic RNA exosome., Liu Q, Greimann JC, Lima CD, Cell. 2006 Dec 15;127(6):1223-37. PMID:17174896
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (349 Kb) [Save to disk]
  • Biological Unit Coordinates (2nn6.pdb1.gz) 341 Kb
  • CSU: Contacts of Structural Units for 2NN6
  • Structure Factors (725 Kb)
  • Retrieve 2NN6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NN6 from S2C, [Save to disk]
  • Re-refined 2nn6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NN6 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 2NN6
  • 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
  • 3D motif for 2NN6, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nn6_E] [2nn6_C] [2nn6] [2nn6_F] [2nn6_I] [2nn6_B] [2nn6_D] [2nn6_A] [2nn6_G] [2nn6_H]
  • SWISS-PROT database: [Q9Y3B2] [Q13868] [Q9NQT5] [Q9NPD3] [Q9NQT4] [Q5RKV6] [Q15024] [Q96B26] [Q06265]
  • Domain organization of [EXOS1_HUMAN] [EXOS2_HUMAN] [EXOS3_HUMAN] [EXOS4_HUMAN] [EXOS5_HUMAN] [EXOS6_HUMAN] [EXOS7_HUMAN] [EXOS8_HUMAN] [EXOS9_HUMAN] by SWISSPFAM
  • Domain found in 2NN6: [S1 ] by SMART
  • Other resources with information on 2NN6
  • Community annotation for 2NN6 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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