1NIK Transcription date Dec 24, 2002
title Wild Type Rna Polymerase II
authors D.A.Bushnell, R.D.Kornberg
compound source
Molecule: Rpb1
Chain: A
Synonym: Dna-Directed Rna Polymerase II Largest Subunit
Ec: 2.7.7.6
 Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Orf Yor151c
Chain: B
Synonym: 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, Chain Rpb3
Chain: C
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb4
Chain: D
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb5
Chain: E
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase I, II And III 23 Kda Polypeptide;
Chain: F
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb7
Chain: G
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase Subunit Rpb8
Chain: H
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb9
Chain: I
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb10
Chain: J
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb11
Chain: K
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II, Chain Rpb12
Chain: L
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 0.334 R_Free 0.360
crystal
cell
length a length b length c angle alpha angle beta angle gamma
224.098 394.462 284.343 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.10 Å
ligand 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...


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


    • F
  • 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, 12-subunit RNA polymerase II at 4.1-A resolution: implications for the initiation of transcription., Bushnell DA, Kornberg RD, Proc Natl Acad Sci U S A 2003 Jun 10;100(12):6969-73. PMID:12746498
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (536 Kb) [Save to disk]
  • Biological Unit Coordinates (1nik.pdb1.gz) 526 Kb
  • LPC: Ligand-Protein Contacts for 1NIK
  • CSU: Contacts of Structural Units for 1NIK
  • Likely Quarternary Molecular Structure file(s) for 1NIK
  • Structure Factors (675 Kb)
  • Retrieve 1NIK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NIK from S2C, [Save to disk]
  • Re-refined 1nik structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NIK 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 1NIK
  • 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
  • 3D motif for 1NIK, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nika_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nikb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1nikc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nikd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1nike_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1nikf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1nikg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1nikh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1niki_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1nikj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1nikk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1nikl_, region L [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nik_E] [1nik_L] [1nik_A] [1nik_F] [1nik_B] [1nik_J] [1nik_G] [1nik_K] [1nik_H] [1nik] [1nik_I] [1nik_C] [1nik_D]
  • SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P27999]
  • Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB9_YEAST] by SWISSPFAM
  • Domains found in 1NIK: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
    • Other resources with information on 1NIK
  • Community annotation for 1NIK 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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