3J0K Transferase Transcription date Oct 04, 2011
title Orientation Of Rna Polymerase II Within The Human Vp16-Media II-Tfiif Assembly
authors C.Bernecky, P.Grob, C.C.Ebmeier, E.Nogales, D.J.Taatjes
compound source
Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Ec: 2.7.7.6
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerase II 140 Kda Polypeptid
Chain: B
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerase II 45 Kda Polypeptide
Chain: C
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerase II 32 Kda Polypeptide
Chain: D
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kd Polypeptide;
Chain: E
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kd Polypeptide;
Chain: F
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerase II 19 Kda Polypeptide
Chain: G
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Polypeptide;
Chain: H
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerase II Subunit 9
Chain: I
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerases IIIIII Subunit 10
Chain: J
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerase II 13.6 Kda Polypepti
Chain: K
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus

Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 K Polypeptide;
Chain: L
Ec: 2.7.7.6
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Cell_line: Hela
Organelle: Nucleus
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 36.00 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B
  • RNA-directed 5'-3' RNA polym...


    • C


    D
  • RNA-directed 5'-3' RNA polym...


    • E
  • RNA-directed 5'-3' RNA polym...


    • F


    G
  • RNA-directed 5'-3' RNA polym...


    • H
  • RNA-directed 5'-3' RNA polym...


    • I
  • RNA-directed 5'-3' RNA polym...


    • J
  • RNA-directed 5'-3' RNA polym...

  • DNA-directed RNA polymerase ...
    • K
  • RNA-directed 5'-3' RNA polym...


    • L


    Primary referenceMolecular architecture of the human Mediator-RNA polymerase II-TFIIF assembly., Bernecky C, Grob P, Ebmeier CC, Nogales E, Taatjes DJ, PLoS Biol. 2011 Mar;9(3):e1000603. Epub 2011 Mar 29. PMID:21468301
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (641 Kb) [Save to disk]
  • Biological Unit Coordinates (3j0k.pdb1.gz) 634 Kb
  • LPC: Ligand-Protein Contacts for 3J0K
  • CSU: Contacts of Structural Units for 3J0K
  • Retrieve 3J0K in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3J0K from S2C, [Save to disk]
    • View 3J0K in 3D
  • Proteopedia, because life has more than 2D.
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  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 3J0K
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3J0K, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3j0k_C] [3j0k_E] [3j0k_D] [3j0k_H] [3j0k_G] [3j0k] [3j0k_I] [3j0k_J] [3j0k_L] [3j0k_K] [3j0k_A] [3j0k_B] [3j0k_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3J0K: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
    • Other resources with information on 3J0K
  • Community annotation for 3J0K at PDBWiki (http://pdbwiki.org)
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