6D6Q Hydrolase date Apr 22, 2018
title Human Nuclear Exosome-Mtr4 Rna Complex - Overall Reconstruct
authors E.M.Weick, C.D.Lima
compound source
Molecule: Exosome Complex Component Rrp45
Chain: A
Synonym: Exosc9,Autoantigen Pmscl 1,Exosome Component 9,P7 Polymyositis-Scleroderma Overlap Syndrome-Associated Autoan Polymyositisscleroderma Autoantigen 1,Polymyositissclerod Autoantigen 75 Kda,Pmscl-75;
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc9, Pmscl1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp41
Chain: B
Synonym: Exosc4,Exosome Component 4,Ribosomal Rna-Processin 41,P12a;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc4, Rrp41, Ski6
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp43
Chain: C
Synonym: Exosc8,Exosome Component 8,Opa-Interacting Protein Ribosomal Rna-Processing Protein 43,P9;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc8, Oip2, Rrp43
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp46
Chain: D
Synonym: Exosc5,Chronic Myelogenous Leukemia Tumor Antigen Component 5,Ribosomal Rna-Processing Protein 46,P12b;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc5, Cml28, Rrp46
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp42
Chain: E
Synonym: Exosc7,Exosome Component 7,Ribosomal Rna-Processin 42,P8;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc7, Kiaa0116, Rrp42
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Mtr3
Chain: F
Synonym: Exosc6,Exosome Component 6,Mrna Transport Regulato Homolog,Hmtr3,P11;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc6, Mtr3
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp40
Chain: G
Synonym: Exosc3,Exosome Component 3,Ribosomal Rna-Processin 40,P10;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc3, Rrp40, Cgi-102
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Rrp4
Chain: H
Synonym: Exosc2,Exosome Component 2,Ribosomal Rna-Processin 4;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc2, Rrp4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Component Csl4
Chain: I
Synonym: Exosc1,Exosome Component 1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc1, Csl4, Cgi-108
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Component 10
Chain: J
Synonym: Exosc10,Autoantigen Pmscl 2,P100 Polymyositis-Scl Overlap Syndrome-Associated Autoantigen,Polymyositissclero Autoantigen 100 Kda,Pmscl-100,Polymyositisscleroderma Aut 2;
Ec: 3.1.13.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Exosc10, Pmscl, Pmscl2, Rrp6
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Complex Exonuclease Rrp44
Chain: K
Synonym: Dis3,Protein Dis3 Homolog,Ribosomal Rna-Processing 44;
Ec: 3.1.13.-,3.1.26.-
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dis3, Kiaa1008, Rrp44
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: M-Phase Phosphoprotein 6
Chain: L
Synonym: Mpp6, Mphosph6
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mphosph6, Mpp6
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Exosome Rna Helicase Mtr4
Chain: M
Synonym: Mtr4, Mtrex,Atp-Dependent Rna Helicase Dob1,Atp-De Rna Helicase Skiv2l2,Superkiller Viralicidic Activity 2-Lik Like Complex Helicase;
Ec: 3.6.4.13
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Mtrex, Dob1, Kiaa0052, Mtr4, Skiv2l2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna (5'-R(Apgpcpapcpcpgpupapapapgpap 3');
Chain: N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dnarna (62-Mer)
Chain: O
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.45 Å
ligand ANP, MG, ZN enzyme Hydrolase E.C.3.1.13 BRENDA
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


    • J


    K
  • 3'-5'-exoribonuclease activi...
  • nuclease activity
  • endonuclease activity
  • exonuclease activity
  • ribonuclease activity


    • L


    M

  • catalytic step 2 spliceosome...
    • Primary referenceHelicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex., Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia MA, Lima CD, Cell. 2018 Jun 14;173(7):1663-1677.e21. doi: 10.1016/j.cell.2018.05.041. PMID:29906447
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (579 Kb) [Save to disk]
  • Biological Unit Coordinates (6d6q.pdb1.gz) 566 Kb
  • LPC: Ligand-Protein Contacts for 6D6Q
  • CSU: Contacts of Structural Units for 6D6Q
  • Retrieve 6D6Q in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6D6Q from S2C, [Save to disk]
    • View 6D6Q 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 6D6Q
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6d6q_E] [6d6q_J] [6d6q_F] [6d6q_N] [6d6q_H] [6d6q_D] [6d6q_B] [6d6q_I] [6d6q_M] [6d6q_K] [6d6q_C] [6d6q_G] [6d6q_L] [6d6q_A] [6d6q_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 6D6Q
  • Community annotation for 6D6Q at PDBWiki (http://pdbwiki.org)

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science