6BM2 Transcription date Nov 13, 2017
title Pol II Elongation Complex With An Abasic Lesion At I-1 Posit
authors W.Wang, D.Wang
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpo21
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb2
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb3, Yil021w
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb5
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpo26
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb8, Yor224c, Yor50-14
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb9
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb10, Yor210w
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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;
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpb11, Yol005c
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Rpc10, Rpb12, Yhr143w-A, Yhr143bw
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932

Molecule: Dna (5'-D(Pcpap(3dr)Pcptpcptptpgpaptp
Chain: T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Apupcpapapgpapgpa)-3')
Chain: R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: C 1 2 1
R_factor 0.219 R_Free 0.244
crystal
cell
length a length b length c angle alpha angle beta angle gamma
169.110 222.270 193.710 90.00 101.28 90.00
method X-Ray Diffractionresolution 3.40 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...


  • 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 referenceStructural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II., Wang W, Walmacq C, Chong J, Kashlev M, Wang D, Proc Natl Acad Sci U S A. 2018 Feb 27. pii: 1722050115. doi:, 10.1073/pnas.1722050115. PMID:29487211
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1218 Kb) [Save to disk]
  • Biological Unit Coordinates (6bm2.pdb1.gz) 1197 Kb
  • CSU: Contacts of Structural Units for 6BM2
  • Structure Factors (1009 Kb)
  • Retrieve 6BM2 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6BM2 from S2C, [Save to disk]
  • View 6BM2 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 6BM2
  • 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 6bm2 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6bm2_C] [6bm2_K] [6bm2_T] [6bm2_F] [6bm2_E] [6bm2_H] [6bm2_L] [6bm2_B] [6bm2_I] [6bm2_J] [6bm2_A] [6bm2_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6BM2
  • Community annotation for 6BM2 at PDBWiki (http://pdbwiki.org)

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