3CQZ Transcription Toxin date Apr 03, 2008
title Crystal Structure Of 10 Subunit Rna Polymerase II In Complex Inhibitor Alpha-Amanitin
authors C.D.Kaplan, K.M.Larsson, R.D.Kornberg
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1, Rna Polymerase II Su Dna-Directed Rna Polymerase III Largest Subunit, B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit B3, Rna Polymerase II Su Dna-Directed Rna Polymerase II 45 Kda Polypeptide, B44.5;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Dna- Rna Polymerases I, II, And III 14.5 Kda Polypeptide, Abc14. Abc14.4;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Brewer'S Yeast, Lager Beer Yeast, Yeast
Organism_taxid: 4932

Molecule: Alpha-Amanitin
Chain: M
Synonym: Amatoxin, Alpha Amanitin
Engineered: Yes

Synthetic: Yes
Organism_scientific: Amanita Phalloides
Organism_taxid: 67723
symmetry Space Group: I 2 2 2
R_factor 0.200 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.510 222.480 374.230 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CSX, HYP, ILX, TRX, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
note 3CQZ is a representative structure
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 referenceThe RNA polymerase II trigger loop functions in substrate selection and is directly targeted by alpha-amanitin., Kaplan CD, Larsson KM, Kornberg RD, Mol Cell. 2008 Jun 6;30(5):547-56. PMID:18538653
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (554 Kb) [Save to disk]
  • Biological Unit Coordinates (3cqz.pdb1.gz) 542 Kb
  • LPC: Ligand-Protein Contacts for 3CQZ
  • CSU: Contacts of Structural Units for 3CQZ
  • Likely Quarternary Molecular Structure file(s) for 3CQZ
  • Structure Factors (964 Kb)
  • Retrieve 3CQZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3CQZ from S2C, [Save to disk]
  • Re-refined 3cqz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3CQZ 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 3CQZ
  • 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 3CQZ, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3cqz_F] [3cqz_J] [3cqz_I] [3cqz_C] [3cqz_B] [3cqz_M] [3cqz_L] [3cqz_E] [3cqz] [3cqz_H] [3cqz_K] [3cqz_A]
  • 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 3CQZ: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 3CQZ
  • Community annotation for 3CQZ 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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