3GTM Transcription, Transferase Dna-Rna Hybri date Mar 27, 2009
title Co-Complex Of Backtracked Rna Polymerase II With Tfiis
authors D.Wang, D.A.Bushnell, X.Huang, K.D.Westover, M.Levitt, R.D.Kornbe
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Fragment: Dna-Directed Rna Polymerase II Largest Subunit
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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Fragment: Dna-Directed Rna Polymerase II 140 Kda Polypeptid
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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Fragment: Dna-Directed Rna Polymerase II 45 Kda Polypeptide

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

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Fragment: Dna-Directed Rna Polymerases I, II, And III 27 Kd Polypeptide;

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

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Fragment: Dna-Directed Rna Polymerases I, II, And III 23 Kd Polypeptide;

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

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Fragment: Dna-Directed Rna Polymerases I, II, And III 14.5 Polypeptide;
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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Fragment: Dna-Directed Rna Polymerase II Subunit 9
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

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Fragment: Dna-Directed Rna Polymerases IIIIII Subunit 10
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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Fragment: Dna-Directed Rna Polymerase II 13.6 Kda Polypepti
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

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L
Fragment: Dna-Directed Rna Polymerases I, II, And III 7.7 K Polypeptide;
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

Molecule: Transcription Elongation Factor S-II
Chain: S
Fragment: Transcription Factor Iis E291h Mutation, Unp Resi 309;
Synonym: Dna Strand Transfer Protein Alpha,Stp-Alpha,Dna St Transferase 1,Pyrimidine Pathway Regulatory Protein 2;
Engineered: Yes
Mutation: Yes

Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c);
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Gene: Dst1, Ppr2, Ygl043w
Expression_system: Escherichia Coli
Expression_system_taxid: 511693
Expression_system_strain: Bl21

Molecule: Rna (5'-R(Apupcpgpapgpapgpgpapupgpc)
Chain: M
Fragment: Rna Strand
Engineered: Yes
Other_details: Rna Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Rna

Molecule: Dna (28-Mer)
Chain: N
Fragment: Dna Template Strand
Engineered: Yes
Other_details: Dna Template Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Template Dna

Molecule: Dna (5'-D(Cptpgpcptptpaptpcpgpgptpap
Chain: O
Fragment: Dna Non-Template Strand
Engineered: Yes
Other_details: Dna Non-Template Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Non-Template Dna
symmetry Space Group: C 1 2 1
R_factor 0.234 R_Free 0.289
crystal
cell
length a length b length c angle alpha angle beta angle gamma
172.329 218.530 193.913 90.00 100.32 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand 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...


  • S


    Primary referenceStructural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution., Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD, Science. 2009 May 29;324(5931):1203-6. PMID:19478184
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1288 Kb) [Save to disk]
  • Biological Unit Coordinates (3gtm.pdb1.gz) 1276 Kb
  • LPC: Ligand-Protein Contacts for 3GTM
  • CSU: Contacts of Structural Units for 3GTM
  • Likely Quarternary Molecular Structure file(s) for 3GTM
  • Structure Factors (1154 Kb)
  • Retrieve 3GTM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GTM from S2C, [Save to disk]
  • Re-refined 3gtm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GTM 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 3GTM
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3GTM, from MSDmotif at EBI
  • Fold representative 3gtm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gtm_I] [3gtm_L] [3gtm_B] [3gtm_A] [3gtm] [3gtm_C] [3gtm_F] [3gtm_K] [3gtm_M] [3gtm_J] [3gtm_E] [3gtm_O] [3gtm_H] [3gtm_N] [3gtm_S]
  • SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P27999] [P07273]
  • Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB9_YEAST] [TFS2_YEAST] by SWISSPFAM
  • Domains found in 3GTM: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [TFS2M] [ZnF_C2C2 ] by SMART
  • Other resources with information on 3GTM
  • Community annotation for 3GTM at PDBWiki (http://pdbwiki.org)
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