1Y1W Transcription,Transferase Dna-Rna Hybrid date Nov 19, 2004
title Complete Rna Polymerase II Elongation Complex
authors P.Cramer, H.Kettenberger, K.J.Armache
compound source
Molecule: 5'- D(Papgptpapcptptpapcpgpcpcptpgpgptpcpapt )-3';
Chain: T
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-D(Apapgptpapcpt)-3'
Chain: N
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: 5'-R(Apapgpapcpcpapgpgpc)-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Other_details: Synthetic Oligonucleotide

Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Synonym: Rna Polymerase II Subunit 1, B220
Ec: 2.7.7.6

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

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

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

Molecule: Dna-Directed Rna Polymerase II 45 Kda Polypeptide;
Chain: C
Synonym: B44.5
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerase II 32 Kda Polypeptide;
Chain: D
Synonym: B32
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kda Polypeptide;
Chain: E
Synonym: Abc27
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kda Polypeptide;
Chain: F
Synonym: Abc23
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerase II 19 Kda Polypeptide;
Chain: G
Synonym: B16
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Kda Polypeptide;
Chain: H
Synonym: Abc14.4
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerase II Subunit 9
Chain: I
Synonym: Dna-Directed Rna Polymerase II 14.2 Kda Polypeptide, B12.6;
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerases IIIIII Subunit 10
Chain: J
Synonym: Dna- Directed Rna Polymerases I, II, And III 8.3 Kda Polypeptide, Abc10- Beta, Abc8;
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerase II 13.6 Kda Polypeptide;
Chain: K
Synonym: B13.6
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 Kda Polypeptide;
Chain: L
Synonym: Abc10-Alpha
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: C 2 2 21
R_factor 0.253 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
221.370 392.500 283.180 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.00 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • RNA-directed 5'-3' RNA polym...


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


  • 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...


  • Primary referenceComplete RNA Polymerase II Elongation Complex Structure and Its Interactions with NTP and TFIIS., Kettenberger H, Armache KJ, Cramer P, Mol Cell 2004 Dec 22;16(6):955-65. PMID:15610738
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (667 Kb) [Save to disk]
  • Biological Unit Coordinates (1y1w.pdb1.gz) 647 Kb
  • LPC: Ligand-Protein Contacts for 1Y1W
  • CSU: Contacts of Structural Units for 1Y1W
  • Likely Quarternary Molecular Structure file(s) for 1Y1W
  • Structure Factors (1029 Kb)
  • Retrieve 1Y1W in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y1W from S2C, [Save to disk]
  • Re-refined 1y1w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y1W 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 1Y1W
  • 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 1Y1W, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1y1wa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1y1wb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1y1wc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1y1wd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1y1we_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1y1wf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1y1wg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1y1wh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1y1wi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1y1wj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1y1wk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1y1wl_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1y1w from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y1w_J] [1y1w_F] [1y1w_T] [1y1w_P] [1y1w_N] [1y1w_C] [1y1w_E] [1y1w_B] [1y1w_K] [1y1w] [1y1w_L] [1y1w_I] [1y1w_G] [1y1w_A] [1y1w_D] [1y1w_H]
  • SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P20433] [P34087] [P27999]
  • Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB4_YEAST] [RPB7_YEAST] [RPB9_YEAST] by SWISSPFAM
  • Domains found in 1Y1W: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 1Y1W
  • Community annotation for 1Y1W at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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