5FLM Transcription date Oct 26, 2015
title Structure Of Transcribing Mammalian Rna Polymerase II
authors C.Bernecky, F.Herzog, W.Baumeister, J.M.Plitzko, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase
Chain: A
Ec: 2.7.7.6
 Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Dna-Directed Rna Polymerase II 140 Kda Polypeptide Directed Rna Polymerase II Subunit B, Rna Polymerase II Sub Rna Polymerase II Subunit B2;
Ec: 2.7.7.6
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit B3, Dna-Directed Rna Pol Subunit C;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Rna Polymerase II Subunit B4, Dna-Directed Rna Pol Subunit D, Rna Polymerase II 16 Kda Subunit, Rpb16;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Dna-D Rna Polymerase II Subunit E, Rpb5 Homolog;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Dna-D Rna Polymerase II Subunit F, Rpb6 Homolog;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7, Dna-Directed Rna Pol Subunit G;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Dna-D Rna Polymerase II Subunit H, Dna-Directed Rna Polymerases I 17.1 Kda Polypeptide, Rpb17, Rpb8 Homolog, Hrpb8;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, Dna-Directed Rna Pol Subunit I;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, Dna-D Rna Polymerase III Subunit L;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, Dna-Directed Rna Po II Subunit J;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Dna-D Rna Polymerase II Subunit K;
Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913
Tissue: Thymus

Molecule: Dna, Dna-Rna Elongation Scaffold
Chain: N
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna, Dna-Rna Elongation Scaffold
Chain: P
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna, Dna-Rna Elongation Scaffold
Chain: T
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 3.40 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F


G


H


I


J


K


L


Primary referenceStructure of transcribing mammalian RNA polymerase II., Bernecky C, Herzog F, Baumeister W, Plitzko JM, Cramer P, Nature. 2016 Jan 28;529(7587):551-4. doi: 10.1038/nature16482. Epub 2016 Jan 20. PMID:26789250
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (616 Kb) [Save to disk]
  • Biological Unit Coordinates (5flm.pdb1.gz) 606 Kb
  • LPC: Ligand-Protein Contacts for 5FLM
  • CSU: Contacts of Structural Units for 5FLM
  • Retrieve 5FLM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5FLM from S2C, [Save to disk]
    • View 5FLM 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 5FLM
  • 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: [5flm_E] [5flm_N] [5flm_J] [5flm_H] [5flm_C] [5flm_G] [5flm_F] [5flm] [5flm_I] [5flm_K] [5flm_T] [5flm_L] [5flm_A] [5flm_P] [5flm_B] [5flm_D]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5FLM: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
    • Other resources with information on 5FLM
  • Community annotation for 5FLM at PDBWiki (http://pdbwiki.org)

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