1NT9 Transcription, Transferase date Jan 29, 2003
title Complete 12-Subunit Rna Polymerase II
authors K.J.Armache, H.Kettenberger, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Synonym: Rpb1; B220
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 45 Kda Polypeptide;
Chain: C
Synonym: Rpb3; B44.5
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Yeast Dna-Directed Rna Polymerase II 32 Kd Polypeptide;
Chain: D
Synonym: Rpb4; B32
Ec: 2.7.7.6
Engineered: Yes
Other_details: Numbering Of Resiudes D10-D24 Is Arbitrary

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kda Polypeptide;
Chain: E
Synonym: Rpb5; Abc27
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kda Polypeptide;
Chain: F
Synonym: Rpb6; Abc23; Rna Polymerase II Sixth Subunit
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 19 Kd Polypeptide
Chain: G
Synonym: Rpb7; B16; Rpb7p
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Kd Polypeptide;
Chain: H
Synonym: Rpb8; Abc14.4; 16-Kda Rna Polymerase Subunit
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 14.2 Kda Polypeptide;
Chain: I
Synonym: Rpb9; B12.6; Rpb9p
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerases I, II, And III 8.3 Kda Polypeptide;
Chain: J
Synonym: Rpb10; Abc10-Beta; Abc8; Rpb10p
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerase II 13.6 Kd Polypeptide;
Chain: K
Synonym: Rpb11; B13.6
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4

Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 Kda Polypeptide;
Chain: L
Synonym: Rpb12; Abc10-Alpha; Rpc10p
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4
symmetry Space Group: C 2 2 21
R_factor
R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
220.400 391.400 282.200 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.20 Å
ligand
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 referenceArchitecture of initiation-competent 12-subunit RNA polymerase II., Armache KJ, Kettenberger H, Cramer P, Proc Natl Acad Sci U S A 2003 Jun 10;100(12):6964-8. PMID:12746495
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (84 Kb) [Save to disk]
  • Biological Unit Coordinates (1nt9.pdb1.gz) 75 Kb
  • CSU: Contacts of Structural Units for 1NT9
  • Likely Quarternary Molecular Structure file(s) for 1NT9
  • Retrieve 1NT9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NT9 from S2C, [Save to disk]
  • View 1NT9 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 1NT9
  • 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
  • 3D motif for 1NT9, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nt9a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nt9b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1nt9c_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nt9d_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1nt9e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1nt9f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1nt9g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1nt9h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1nt9i_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1nt9j_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1nt9k_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1nt9l_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1nt9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nt9_B] [1nt9_L] [1nt9_H] [1nt9_A] [1nt9_F] [1nt9_I] [1nt9_J] [1nt9_D] [1nt9_K] [1nt9_C] [1nt9] [1nt9_G] [1nt9_E]
  • 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 1NT9: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 1NT9
  • Community annotation for 1NT9 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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