6UPX Transcription Rna Dna date Oct 18, 2019
title Rna Polymerase II Elongation Complex With 5-Guanidinohydanto In State 1
authors J.Oh, D.Wang
compound source
Molecule: Rna
Chain: R
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Template Strand Dna
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Non-Template Strand Dna
Chain: N
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1,Dna-Directed Rna Poly Largest Subunit,Rna Polymerase II Subunit B220;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Atcc: 204508
symmetry Space Group: C 1 2 1
R_factor 0.220 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
168.988 223.314 193.102 90.00 101.03 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand G35, 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...


  • 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 referenceRNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions., Oh J, Fleming AM, Xu J, Chong J, Burrows CJ, Wang D, Proc Natl Acad Sci U S A. 2020 Apr 28;117(17):9338-9348. doi:, 10.1073/pnas.1919904117. Epub 2020 Apr 13. PMID:32284409
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1282 Kb) [Save to disk]
  • Biological Unit Coordinates (6upx.pdb1.gz) 1260 Kb
  • LPC: Ligand-Protein Contacts for 6UPX
  • CSU: Contacts of Structural Units for 6UPX
  • Structure Factors (4596 Kb)
  • Retrieve 6UPX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6UPX from S2C, [Save to disk]
  • View 6UPX in 3D
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  • Visual 3D analysis of 6UPX
  • 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
  • Fold representative 6upx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6upx_J] [6upx_B] [6upx_I] [6upx_N] [6upx_A] [6upx_E] [6upx_T] [6upx_F] [6upx_C] [6upx_R] [6upx_H] [6upx_K] [6upx_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6UPX
  • Community annotation for 6UPX at PDBWiki (http://pdbwiki.org)

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