2NN6 Hydrolase Transferase date Oct 23, 2006
title Structure Of The Human Rna Exosome Composed Of Rrp41, Rrp45, Rrp46, 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-75;
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 Component 4, 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 Component 8, 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 Component 5, 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 Component 7, 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 Component 3, 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 Component 2;
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] (359 Kb) [Save to disk]
  • Biological Unit Coordinates (2nn6.pdb1.gz) 346 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
  • 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 2NN6, from MSDmotif at EBI
  • Fold representative 2nn6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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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