5OIK Transcription date Jul 18, 2017
title Structure Of An Rna Polymerase II-Dsif Transcription Elongat Complex
authors C.Bernecky, J.M.Plitzko, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Ec: 2.7.7.6
Organism_scientific: Bos Taurus
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: B
Ec: 2.7.7.6

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit B3,Dna-Directed Rna Poly Subunit C;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Polymerase (Rna) II (Dna Directed) Polypeptide D
Chain: D

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Synonym: Rna Polymerases I,II,And III Subunit Abc1,Dna-Dire Polymerase II Subunit E,Rpb5 Homolog;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7,Dna-Directed Rna Poly Subunit G;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Uncharacterized Protein
Chain: H

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9,Dna-Directed Rna Poly Subunit I;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I,II,And III Subunit Abc5,Dna-Dire Polymerase III Subunit L;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11,Dna-Directed Rna Pol Subunit J;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L
Synonym: Rna Polymerases I,II,And III Subunit Abc4,Dna-Dire Polymerase II Subunit K;

Organism_scientific: Bos Taurus
Organism_common: Bovine
Organism_taxid: 9913

Molecule: Dna (43-Mer)
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'- R(Pupapupapupapcpapupapapapgpapcpcpapgpg
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (43-Mer)
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Transcription Elongation Factor Spt4
Chain: Y
Synonym: Hspt4,Drb Sensitivity-Inducing Factor 14 Kda Subun P14,Drb Sensitivity-Inducing Factor Small Subunit,Dsif Smal
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt4h1, Spt4h, Supt4h
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Ril

Molecule: Transcription Elongation Factor Spt5
Chain: Z
Synonym: Hspt5,Drb Sensitivity-Inducing Factor 160 Kda Subu P160,Drb Sensitivity-Inducing Factor Large Subunit,Dsif Lar Subunit,Tat-Cotransactivator 1 Protein,Tat-Ct1 Protein;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Supt5h, Spt5, Spt5h
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Ril
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 3.70 Å
ligand
enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E
  • RNA polymerase I activity
  • RNA polymerase III activity


  • F
  • RNA polymerase I activity
  • RNA polymerase III activity


  • G


    H
  • RNA polymerase I activity


  • I


    J


    K


    L
  • RNA polymerase I activity
  • RNA polymerase III activity


  • Y


    Z


    Primary referenceStructure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp., Bernecky C, Plitzko JM, Cramer P, Nat Struct Mol Biol. 2017 Sep 11. doi: 10.1038/nsmb.3465. PMID:28892040
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (720 Kb) [Save to disk]
  • Biological Unit Coordinates (5oik.pdb1.gz) 706 Kb
  • CSU: Contacts of Structural Units for 5OIK
  • Retrieve 5OIK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OIK from S2C, [Save to disk]
  • View 5OIK in 3D
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  • 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 5OIK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5oik from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oik_Y] [5oik_H] [5oik_K] [5oik_Z] [5oik_P] [5oik_I] [5oik_J] [5oik_L] [5oik_B] [5oik_A] [5oik_N] [5oik_F] [5oik_G] [5oik_D] [5oik_C] [5oik_T] [5oik_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OIK
  • Community annotation for 5OIK at PDBWiki (http://pdbwiki.org)

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