5OA1 Transcription date Jun 20, 2017
title Rna Polymerase I Pre-Initiation Complex
authors Y.Sadian, L.Tafur, J.Kosinski, A.J.Jakobi, C.W.Muller
compound source
Molecule: Dna-Directed Rna Polymerase I Subunit Rpa190
Chain: A
Synonym: Dna-Directed Rna Polymerase I 190 Kda Polypeptide, Directed Rna Polymerase I Largest Subunit;
Ec: 2.7.7.6
 Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa135
Chain: B
Synonym: Dna-Directed Rna Polymerase I 135 Kda Polypeptide, Directed Rna Polymerase I Polypeptide 2,Rna Polymerase I Su
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerases I And III Subunit Rp
Chain: C
Synonym: Rna Polymerases I And III Subunit Ac1,C37,Dna-Dire Polymerases I And III 40 Kda Polypeptide,C40;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa14
Chain: D
Synonym: A14,Dna-Directed Rna Polymerase I 14 Kda Polypepti
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

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 S288c
Organism_taxid: 559292

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 S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa43
Chain: G
Synonym: A43,Dna-Directed Dna-Dependent Rna Polymerase 36 K Polypeptide;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

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 S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa12
Chain: I
Synonym: A12,A12.2,Dna-Directed Rna Polymerase I 13.7 Kda Polypeptide;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

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 S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerases I And III Subunit Rp
Chain: K
Synonym: Rna Polymerases I And III Subunit Ac2,Ac19,Dna-Dir Polymerases I And III 16 Kda Polypeptide,Rpa19;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

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 S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa49
Chain: M
Synonym: A49,Dna-Directed Rna Polymerase I 49 Kda Polypepti
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa34
Chain: N
Synonym: A34,Dna-Directed Dna-Dependent Rna Polymerase 34.5 Polypeptide,A34.5;
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Rna Polymerase I-Specific Transcription Initiatio Rrn3;
Chain: O
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Dna (49-Mer)
Chain: S
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Dna (56-Mer)
Chain: T
Engineered: Yes
Synthetic: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292

Molecule: Rna Polymerase I-Specific Transcription Initiatio Rrn7;
Chain: U
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Gene: Rrn7, Yjl025w, J1273
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase I-Specific Transcription Initiatio Rrn6;
Chain: V
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Gene: Rrn6, Ybl014c, Ybl0311, Ybl0312
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase I-Specific Transcription Initiatio Rrn11;
Chain: W
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Gene: Rrn11, Yml043c, Ym9827.09c
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A
Chain: 1
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala-Ala-Ala-Ala-Ala;
Chain: 2
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala
Chain: 3, 9
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala;
Chain: 4
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala-Ala;
Chain: 5, Q
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala
Chain: 6, 8
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala;
Chain: 7
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala;
Chain: P
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala;
Chain: Z
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala
Chain: Y
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-Ala-A Ala-Ala-Ala-Ala-Ala-Ala-Ala;
Chain: R
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_taxid: 559292
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 4.40 Å
ligand ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E
  • RNA-directed 5'-3' RNA polym...


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


    • G


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


    • I


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

  • DNA-directed RNA polymerase ...
    • K


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


    • M


    N


    O


    U


    V
  • RNA polymerase I CORE elemen...


    • W
  • RNA polymerase I CORE elemen...


    • Primary referenceStructural insights into transcription initiation by yeast RNA polymerase I., Sadian Y, Tafur L, Kosinski J, Jakobi AJ, Wetzel R, Buczak K, Hagen WJ, Beck M, Sachse C, Muller CW, EMBO J. 2017 Sep 15;36(18):2698-2709. doi: 10.15252/embj.201796958. Epub 2017 Jul, 24. PMID:28739580
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (882 Kb) [Save to disk]
  • Biological Unit Coordinates (5oa1.pdb1.gz) 856 Kb
  • LPC: Ligand-Protein Contacts for 5OA1
  • CSU: Contacts of Structural Units for 5OA1
  • Retrieve 5OA1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OA1 from S2C, [Save to disk]
    • View 5OA1 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 5OA1
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i5oa1, region A:1-150 [Jmol] [rasmolscript] [script source]
        - Domain d1j5oa1, region A:430-558 [Jmol] [rasmolscript] [script source]
        - Domain d1r5oa1, region A:460-554 [Jmol] [rasmolscript] [script source]
        - Domain d1s5oa1, region A:9-385 [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oa1_T] [5oa1_D] [5oa1_3] [5oa1_S] [5oa1_C] [5oa1_L] [5oa1_H] [5oa1_Z] [5oa1_I] [5oa1_A] [5oa1_4] [5oa1_Y] [5oa1_U] [5oa1_8] [5oa1_1] [5oa1_5] [5oa1_W] [5oa1_7] [5oa1_R] [5oa1_J] [5oa1_O] [5oa1_F] [5oa1_M] [5oa1_P] [5oa1_E] [5oa1_6] [5oa1_B] [5oa1_G] [5oa1_K] [5oa1_9] [5oa1_Q] [5oa1_V] [5oa1_2] [5oa1_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5OA1
  • Community annotation for 5OA1 at PDBWiki (http://pdbwiki.org)

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