4BY1 Transcription date Jul 17, 2013
title Elongating Rna Polymerase II-Bye1 Tld Complex Soaked With Am
authors K.Kinkelin, G.G.Wozniak, S.B.Rothbart, M.Lidschreiber, B.D.Strah P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Rna Polymerase II Subunit 2, B150, Dna-Directed Rn Polymerase II 140 Kda Polypeptide;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit 3, Rna Polymerase II Sub B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Rna Polymerase II Subunit B4, B32, Dna-Directed Rn Polymerase II 32 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 1;
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Directed Rna Polymerases I, II, And III 27 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 2;
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Directed Rna Polymerases I, II, And III 23 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7, B16

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 3;
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Abc14 Abc14.5, Dna-Directed Rna Polymerases I, II, And III 14.5 K Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, B12.6, Dna-Directed Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polyme Subunit 9;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 5;
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, Abc10 Abc8, Dna-Directed Rna Polymerases I, II, And III 8.3 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, B13.6, Dna-Directed Polymerase II 13.6 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 4;
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: 5'-D(Apapapgptpapcptptpgpapgpcptp)-
Chain: N
Synonym: Dna Non-Template Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-R(Upupcpgpapcpcpapgpgpap)-3'
Chain: P
Synonym: Rna Product Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Apgpcptpcpapapgptpapcptptpap Tptpcpcpbrupgpgptpcpapapt)-3';
Chain: T
Synonym: Dna Template Strand
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Transcription Factor Bye1
Chain: X
Fragment: Residues 225-370
Synonym: Bypass Of Ess1 Protein 1
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_variant: Ril
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Popinf
symmetry Space Group: C 2 2 21
R_factor 0.175 R_Free 0.206
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.240 391.580 281.020 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand APC, BRU, MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


  • B


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


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


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


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


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


  • X


    Primary referenceStructures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue., Kinkelin K, Wozniak GG, Rothbart SB, Lidschreiber M, Strahl BD, Cramer P, Proc Natl Acad Sci U S A. 2013 Sep 3. PMID:24003114
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1399 Kb) [Save to disk]
  • Biological Unit Coordinates (4by1.pdb1.gz) 1382 Kb
  • LPC: Ligand-Protein Contacts for 4BY1
  • CSU: Contacts of Structural Units for 4BY1
  • Structure Factors (1257 Kb)
  • Retrieve 4BY1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4BY1 from S2C, [Save to disk]
  • Re-refined 4by1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4BY1 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 4BY1
  • 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 4BY1, from MSDmotif at EBI
  • Fold representative 4by1 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4by1_D] [4by1_H] [4by1_P] [4by1_L] [4by1_N] [4by1] [4by1_J] [4by1_G] [4by1_C] [4by1_B] [4by1_E] [4by1_X] [4by1_I] [4by1_A] [4by1_T] [4by1_F] [4by1_K]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4BY1: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [TFS2M] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4BY1
  • Community annotation for 4BY1 at PDBWiki (http://pdbwiki.org)

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